Multiple sequence alignment plays an important role in molecular sequence analysis. An alignment is the arrangement of two (pairwise alignment) or more (multiple alignment) sequences of residues (nucleotides or amino acids) that maximizes the similarities between them. Algorithmically, the problem consists of opening and extending gaps in the sequences to maximize an objective function (measurement of similarity). A simple genetic algorithm was developed and implemented in the software MSA-GA. Genetic algorithms, a class of evolutionary algorithms, are well suited for problems of this nature since residues and gaps are discrete units. An evolutionary algorithm cannot compete in terms of speed with progressive alignment methods but it has the advantage of being able to correct for initially misaligned sequences; which is not possible with the progressive method. This was shown using the BaliBase benchmark, where Clustal-W alignments were used to seed the initial population in MSA-GA, improving outcome.

Problem statement: The parallelization of multiple progressive alignment algorithms is a difficult task. All known methods have strong bottlenecks resulting from synchronization delays. This is even more constraining in distributed memory systems, where message passing also delays the interprocess communication. Despite these drawbacks, parallel computing is becoming increasingly necessary to perform multiple sequence alignment. Approach: In this study, it is introduced a solution for parallelizing multiple progressive alignments in distributed memory systems that overcomes such delays. Results: The proposed approach uses threads to separate actual alignment from synchronization and communication. It also uses a different approach to schedule independent tasks. Conclusion/Recommendations: The approach was intensively tested, producing a performance remarkably better than a largely used algorithm. It is suggested that it can be applied to improve the performance of some multiple alignment tools, ...

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is web ready: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components.. AVAILABILITY AND IMPLEMENTATION: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online.. CONTACT: [email protected].. ...

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is web ready: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components.. AVAILABILITY AND IMPLEMENTATION: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online.. CONTACT: [email protected].. ...

Copyright 2009 by Cymon J. Cox. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. Command line wrapper for the multiple alignment programme MAFFT. http://align.bmr.kyushu-u.ac.jp/mafft/software/ Citations: Katoh, Toh (BMC Bioinformatics 9:212, 2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (describes RNA structural alignment methods) Katoh, Toh (Briefings in Bioinformatics 9:286-298, 2008) Recent developments in the MAFFT multiple sequence alignment program (outlines version 6) Katoh, Toh (Bioinformatics 23:372-374, 2007) Errata PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm) Katoh, Kuma, Toh, Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence ...

We present an application of ABS algorithms for multiple sequence alignment (MSA). The Markov decision process (MDP) based model leads to a linear programming problem (LPP), whose solution is linked to a suggested alignment. The important features of our work include the facility of alignment of multiple sequences simultaneously and no limit ...

Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf to root, based on a guide tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around from the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the

1) Multiple Sequence Alignment and Analysis with Jalview on Thursday 23rd November 2017. Day 1 workshop employs talks and hands-on exercises to help students learn to use Jalview, a versatile protein and nucleic acid sequence alignment and analysis tool developed within the School of Life Sciences. We will cover launching Jalview, accessing sequence, alignment and 3D structure databases, creating, editing and analysing alignments, phylogenetic trees, analysing alignments with 3D structures, and preparation of figures for presentation and publication.. Workshop trainer: Dr Jim Procter and Dr Suzanne Duce. (2) Protein Sequence Analysis on Thursday 30th November 2017. Day 2 workshop aims to give an understanding of how best to use computational methods to make sense of the structure and function of your favourite protein. The workshop will introduce the principles of sequence analysis and its relationship to protein structure and function. It will highlight common methods and tools for protein ...

Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by genomic sequence alignment. Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches biomedical applications. We discuss recent innovative efforts of improving the existing view of network alignment. We conclude with open research questions in comparative biological network research that could further our understanding of principles of life, evolution, disease, and therapeutics.

Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by genomic sequence alignment. Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches biomedical applications. We discuss recent innovative efforts of improving the existing view of network alignment. We conclude with open research questions in comparative biological network research that could further our understanding of principles of life, evolution, disease, and therapeutics.

How can I do multiple sequence alignment of 2000 nucleotide sequence of rabies virus strain consisting of whole genome sequence and complete cds by using MEGA X and also constructing phylogenetic tree by using same MEGA X software?. ...

Hi, Im new to programming so forgive me if I say something obviously stupid. Im interested in writing a program to do some primer-design tasks, among other things. The first thing I want the program to do, however, is a multiple sequence alignment. I realise this is like reinventing the wheel, which Id rather not do. Are there a few standard algorithms out there for this task? What about other standard molecualr biology algorithms? Also, maybe someone could suggest a few good beginning references for this sort of programing. Thanks! -- Susan http://www4.ncsu.edu/unity/users/s/sjhogart/public/home.html Check this! http://homepage.cistron.nl/~peterh/gsresources/ ...

Tools for Bioinformatics: DNA Sequence Analysis - Features of DNA sequence analysis, Approaches to EST analysis; Pairwise alignment techniques: Comparing two sequences, PAM and BLOSUM, Global alignment (The Needleman and Wunsch algorithm), Local Alignment (The Smith-Waterman algorithm), Dynamic programming, Pairwise database searching: Sequence analysis- BLAST and other related tools, Different methods of Multiple sequence alignment, Searching databases with multiple alignments; Alignment Scores, Design and Analysis of microarray experiments. ...

From evolutionary interference, function annotation to structural prediction, protein sequence comparison has provided crucial biological insights. While many sequence alignment algorithms have been developed, existing approaches are often incapable of detecting hidden structural relationships in the twilight zone of low sequence identity. To address this critical problem, we introduce a computational algorithm that performs protein Sequence Alignments from deep-Learning of Structural Alignments (SAdLSA, silent d). The key idea is to implicitly learn the protein folding code from many thousands of structural alignments. We demonstrate that our models trained on Α-helical domains can be successfully transferred to recognize sequences encoding Β-sheet domains. Training and benchmarking on a larger, highly challenging data sets shows significant improvement over established approaches.. Notice: This server is freely available to all academic and non-commercial users ...

Regina Barzilay of MIT and Lillian Lee of Cornell University have developed a computer program that can automatically paraphrase English sentences: The program culls text from online news services on particular topics, determines distinguishing sentence patterns in these clusters, and employs these patterns to generate new sentences that convey the same message with different wording. Potential applications for such a tool include report summarization, document checking for repetition or plagiarism, and a way for authors to automatically rewrite their prose to readers of different backgrounds, which Lee describes as a style dial. Kevin Knight of the University of Southern California remarks that the program may even be able to help facilitate machine translation. Barzilay and Lee tested the program by having a computer categorize Agence France-Presse and Reuters articles according to subject, and then look for sentence clusters possessing similar words and phrases; the researchers used a ...

TY - JOUR. T1 - Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrroly-sine containing genes. AU - Have, Christian Theil. AU - Zambach, Sine. AU - Christiansen, Henning. PY - 2013. Y1 - 2013. N2 - BackgroundPyrrolysine (the 22nd amino acid) is in certain organisms and under certain circumstances encoded by the amber stop codon, UAG. The circumstances driving pyrrolysine translation are not well understood. The involvement of a predicted mRNA structure in the region downstream UAG has been suggested, but the structure does not seem to be present in all pyrrolysine incorporating genes.ResultsWe propose a strategy to predict pyrrolysine encoding genes in genomes of archaea and bacteria. We cluster open reading frames interrupted by the amber codon based on sequence similarity. We rank these clusters according to several features that may influence pyrrolysine translation. The ranking effects of different features are assessed and we propose a ...

RNALogo: a new approach to display structural RNA alignment - Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to create a new graphical representation of the patterns in a multiple RNA sequence alignment with a consensus structure. The RNALogo graph can indicate significant features within an RNA sequence alignment and its consensus RNA secondary structure. RNALogo extends Sequence logos, and specifically incorporates RNA secondary structures and mutual information of base-paired regions into the graphical representation. Each RNALogo graph is composed of stacks of letters, with one stack for each position in the consensus RNA secondary structure. RNALogo provides a convenient and high configurable logo generator. An RNALogo graph is generated for each RNA family in Rfam, and these generated logos are accumulated into a gallery of RNALogo. Users can search or browse RNALogo

BACKGROUND: The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments.. RESULTS: Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using ...

Publications, Genomes and Genes, Scientific Experts, Species, Research Topics, Locale about Experts and Doctors on sequence alignment in Mississippi, United States

DIALIGN is a software program for multiple sequence alignment developed by Burkhard Morgensternet al.. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies.. The latest version of the program, DIALIGN-TX, is described in Subramanian et al. (2008), Algorithms Mol. Biol. 3:6. A web server for this program is available at Goettingen Bioinformatics Compute Server (GOBICS). A web server for multiple alignment with user-defined constraints (anchor points) as described by Morgenstern et al. (2006), Algorithms Mol. Biol. 1:6 is also available through GOBICS.. During the last few years, DIALIGN has been successfully used by many researchers to align genomic sequences; some break-through ...

DIALIGN is a software program for multiple sequence alignment developed by Burkhard Morgensternet al.. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies.. The latest version of the program, DIALIGN-TX, is described in Subramanian et al. (2008), Algorithms Mol. Biol. 3:6. A web server for this program is available at Goettingen Bioinformatics Compute Server (GOBICS). A web server for multiple alignment with user-defined constraints (anchor points) as described by Morgenstern et al. (2006), Algorithms Mol. Biol. 1:6 is also available through GOBICS.. During the last few years, DIALIGN has been successfully used by many researchers to align genomic sequences; some break-through ...

Jalview http://www.jalview.org/ https://tess.elixir-europe.org/content_providers/jalview Jalview (www.jalview.org) is free-to-use sequence alignment and analysis visualisation software that links genomic variants, protein alignments and 3D structure. Protein, RNA and DNA data can be directly accessed from public databases (e.g. Pfam, Rfam, PDB, UniProt and ENA etc.). Jalview has editing and annotation functionality within a fully integrated, multiple window interface. The sequence alignment programs Clustal Omega, Muscle, MAFFT, ProbCons, T-COFFEE, ClustalW, MSA Prob and GLProb can be run directly from within Jalview. Jalview integrates protein secondary structure prediction (JPred), generate trees, assesses consensus and conservation across sequence families. Journal quality figures can be generated from the results. The Jalview Desktop will run on Mac, MS Windows, Linux and any other platform that supports Java. It has been developed in Geoff Bartons group (www.compbio.dundee.ac.uk) in the ...

Jalview http://www.jalview.org/ https://tess.elixir-europe.org/content_providers/jalview Jalview (www.jalview.org) is free-to-use sequence alignment and analysis visualisation software that links genomic variants, protein alignments and 3D structure. Protein, RNA and DNA data can be directly accessed from public databases (e.g. Pfam, Rfam, PDB, UniProt and ENA etc.). Jalview has editing and annotation functionality within a fully integrated, multiple window interface. The sequence alignment programs Clustal Omega, Muscle, MAFFT, ProbCons, T-COFFEE, ClustalW, MSA Prob and GLProb can be run directly from within Jalview. Jalview integrates protein secondary structure prediction (JPred), generate trees, assesses consensus and conservation across sequence families. Journal quality figures can be generated from the results. The Jalview Desktop will run on Mac, MS Windows, Linux and any other platform that supports Java. It has been developed in Geoff Bartons group (www.compbio.dundee.ac.uk) in the ...

Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences. A comparison of the frequency of sequence alignments, determined by MegaBLAST, between rice coding sequences in TIGR pseudomolecules and annotations vs 4.0 and comprehensive transcript-assembly and methylation-filtered databases from Lolium perenne (ryegrass), Zea mays (maize), Hordeum vulgare (barley), Glycine max (soybean) and Arabidopsis thaliana (thale cress) was undertaken. Each rice pseudomolecule was divided into 10 segments, each containing 10% of the functionally annotated, expressed genes. This indicated a correlation between relative segment position in the rice genome and numbers of alignments with all the queried monocot and dicot plant databases. Colour-coded moving windows of 100 functionally

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent …

Recent methods have been developed to perform high-throughput sequencing of DNA by Single Molecule Sequencing (SMS). While Next-Generation sequencing methods may produce reads up to several hundred bases long, SMS sequencing produces reads up to tens of kilobases long. Existing alignment methods are either too inefficient for high-throughput datasets, or not sensitive enough to align SMS reads, which have a higher error rate than Next-Generation sequencing. We describe the method BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error. The method is benchmarked using both simulated reads and reads from a bacterial sequencing project. We also present a combinatorial model of sequencing error that motivates why our approach is effective. The results indicate that it is possible to map SMS reads with high accuracy and speed. Furthermore,

Recent methods have been developed to perform high-throughput sequencing of DNA by Single Molecule Sequencing (SMS). While Next-Generation sequencing methods may produce reads up to several hundred bases long, SMS sequencing produces reads up to tens of kilobases long. Existing alignment methods are either too inefficient for high-throughput datasets, or not sensitive enough to align SMS reads, which have a higher error rate than Next-Generation sequencing. We describe the method BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error. The method is benchmarked using both simulated reads and reads from a bacterial sequencing project. We also present a combinatorial model of sequencing error that motivates why our approach is effective. The results indicate that it is possible to map SMS reads with high accuracy and speed. Furthermore,

Another possibility is to use bioedit that is a alignemnt sequence editor software. this allows easily to align by Clustal the selected sequences and also is possible to performs blast searches directly rom the main windows, retrieve sequences (with all the GenBank information) directli from NCBI and align again... if well setted is also possible to use the complete phylip package to make trees ...

Fig. 1. Phylogram demonstrating amino acid sequence identity among Cry and Cyt proteins. This phylogenetic tree is modified from a TREEVIEW visualization of NEIGHBOR treatment of a CLUSTAL W multiple alignment and distance matrix of the full-length toxin sequences, as described in the text. The gray vertical bars demarcate the four levels of nomenclature ranks. Based on the low percentage of identical residues and the absence of any conserved sequence blocks in multiple-sequence alignments, the lower four lineages are not treated as part of the main toxin family, and their nodes have been replaced with dashed horizontal lines in this figure. ...

Find similarities between texts using the Smith-Waterman algorithm. The algorithm performs local sequence alignment and determines similar regions between two strings. The Smith-Waterman algorithm is explained in the paper: Identification of common molecular subsequences by T.F.Smith and M.S.Waterman (1981), available at ,doi:10.1016/0022-2836(81)90087-5,. This package implements the same logic for sequences of words and letters instead of molecular sequences.. ...

A key element in evaluating the quality of a pairwise sequence alignment is the substitution matrix, which assigns a score for aligning any possible pair of residues. The theory of amino acid substitution matrices is described in [1], and applied to DNA sequence comparison in [2]. In general, different substitution matrices are tailored to detecting similarities among sequences that are diverged by differing degrees [1-3]. A single matrix may nevertheless be reasonably efficient over a relatively broad range of evolutionary change [1-3]. Experimentation has shown that the BLOSUM-62 matrix [4] is among the best for detecting most weak protein similarities. For particularly long and weak alignments, the BLOSUM-45 matrix may prove superior. A detailed statistical theory for gapped alignments has not been developed, and the best gap costs to use with a given substitution matrix are determined empirically. Short alignments need to be relatively strong (i.e. have a higher percentage of matching ...

TY - JOUR. T1 - Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion. AU - Thomsen, Martin Christen Frølund. AU - Nielsen, Morten. PY - 2012. Y1 - 2012. N2 - Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving ...

This track shows multiple alignments of 100 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track. PHAST/Multiz are built from chains (alignable) and nets (syntenic), see the documentation of the Chain/Net tracks for a description of the complete alignment process. PhastCons is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth ...

Myoskeletal Alignment Techniques is a term first coined by Dalton in the early 1980s. However, Dalton never stops developing the MAT system. Over the years, the work of Phillip Greenman, Serge Gracovetsky and many other visionaries in kinesiology and human performance have been integrated into his training programs. By teaching how to identify and correct dysfunctional, neurologically-driven strain patterns before they become pain patterns, he has created one of the most integrative and complete perspectives on pain management.. MAT practitioners learn how to take clients through a series of sessions in deep tissue therapy that calms hyper-excited nerve receptors. When the pain-generating stimulus is effectively interrupted, new memories can be programmed into muscle cells by inhibiting the chemical activation of pain, which allows the brain to downgrade its signals for chronic protective spasms.. Of course, effective bodywork depends on much more than intellectual knowledge. Daltons program ...

Link to Pubmed [PMID] - 17359063. Phys. Rev. Lett. 2007 Feb;98(7):078101. Alignment algorithms usually rely on simplified models of gaps for computational efficiency. Based on correspondences between alignments and structural models for nucleic acids, and using methods from statistical mechanics, we show that alignments with realistic laws for gaps can be computed with fast algorithms. Improved performances of probabilistic alignments with realistic models of gaps are illustrated. By contrast with optimization-based alignments, such improvements with realistic laws are not observed. General perspectives for biological and physical modelings are mentioned.. https://www.ncbi.nlm.nih.gov/pubmed/17359063 ...

TY - JOUR. T1 - ArchAlign. T2 - Coordinate-free chromatin alignment reveals novel architectures. AU - Lai, William K.M.. AU - Buck, Michael J.. PY - 2010/12/23. Y1 - 2010/12/23. N2 - To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. We validated ArchAlign using well characterized functional elements, and used it to explore the chromatin structural architecture at CTCF binding sites in the human genome. ArchAlign is freely available at http://www.acsu.buffalo.edu/~mjbuck/ArchAlign.html.. AB - To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared ...

Next Generation Sequencing (NGS) technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/M...read more ...

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We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to ...

generalized Algebraic Dynamic Programming. A selection of (sequence) alignment algorithms. Both terminal, and syntactic variables, as well as the index type is not fixed here. This makes it possible to select the correct structure of the grammar here, but bind the required data type for alignment in user code.. That being said, these algorithms are mostly aimed towards sequence alignment problems.. List of grammars for sequences:. ...

alignment of short DNA sequences The package provices a reimplementation of the Nearest Alignment Space Termination tool in Python. It was prepared for next generation sequencers. Given a set of sequences and a template alignment, PyNAST will align the input sequences against the template alignment, and return a multiple sequence alignment which contains the same number of positions (or columns) as the template alignment. This facilitates the analysis of new sequences in the context of existing alignments, and additional data derived from existing alignments such as phylogenetic trees. Because any protein or nucleic acid sequences and template alignments can be provided, PyNAST is not limited to the analysis of 16s rDNA sequences. ...

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible and used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill ...

2009/8/4 Ryan Golhar ,golharam at umdnj.edu,: ,,, Im trying to perform a large amount of sequence alignments of long DNA ,,, sequences, some up to 163,000+ bp in length. I was trying to use the ,,, standard Needleman-Wunsch algorithm, but the matrix used requires a ,,, large amount of memory...about 100 GB of memory. This obviously wont ,,, work. ,, ,, How many were you trying to align? You mean 163kb or 163Mb? ,, I was looking for test or comparisons for some alignment code I had which ,, indexed the target sequences, dont recall the suggestions ,, for that discussion but I was able to do simple genomes reasonably well ( ,, I think I used 2 strains of e coli or something about 5 megs long) ,, on a desktop. If you can find responses to my request from a few years ago ,, that may ( or may not ) help. Id offer my code, and indeed I think ,, I have it on a website, but I stopped development and not sure ,, it is nearly useful as-is unless you just want coarse alignment on ,, two similar ...

Traditionally, multiple sequence alignment algorithms use computationally complex heuristics to align the sequences. Unfortunately, the use of heuristics do not guarantee global optimization as it would be prohibitively computationally expensive to achieve an optimal alignment. This is due in part to the sheer size of the genome, which consists of roughly three billion base pairs, and the increasing computational complexity resulting from each additional sequence in an alignment.. ...

Concepts and Introduction to RNA Bioinformatics -- The Principles of RNA Structure Architecture -- The Determination of RNA Folding Nearest Neighbor Parameters -- Energy Directed RNA Structure Prediction -- Introduction to Stochastic Context Free Grammars -- An Introduction to RNA Databases -- Energy-based RNA Consensus Secondary Structure Prediction in Multiple Sequence Alignments -- SCFGs in RNA Secondary Structure Prediction: A Hands-on Approach -- Annotating Functional RNAs in Genomes using Infernal -- Class-specific Prediction of ncRNAs -- Abstract Shape Analysis of RNA -- Introduction to RNA Secondary Structure Comparison -- RNA Structural Alignments, Part I: Sankoff Based Approaches for Structural Alignments -- RNA Structural Alignments, Part II: Non-Sankoff Approaches for Structural Alignments -- De novo Discovery of Structured ncRNA Motifs in Genomic Sequences., -- Phylogeny and Evolution of RNA Structure -- The Art of Editing RNA Structural Alignments -- Automated Modeling of RNA 3D ...

This paper describes a novel approach to constructing Position-Specific Weight Matrices (PWMs) based on the transcription factor binding site (TFBS) data provide by the TRANSFAC database and comparison of the newly generated PWMs with the original TRANSFAC matrices. Multiple local sequence alignment was performed on the TFBSs of each transcription factor. Several different alignment programs were tested and their matrices were compared to the original TRANSFAC matrices. One of the alignment programs, GLAM, produced comparable matrices in terms of the average ranking of true positive sites across the whole test set of sequences. ...

In 2000, a fast implementation of the Smith-Waterman algorithm using the SIMD technology available in Intel Pentium MMX processors and similar technology was described in a publication by Rognes and Seeberg.[22] In contrast to the Wozniak (1997) approach, the new implementation was based on vectors parallel with the query sequence, not diagonal vectors. The company Sencel Bioinformatics has applied for a patent covering this approach. Sencel is developing the software further and provides executables for academic use free of charge.. A SSE2 vectorization of the algorithm (Farrar, 2007) is now available providing an 8-16-fold speedup on Intel/AMD processors with SSE2 extensions.[13] When running on Intel processor using the Core microarchitecture the SSE2 implementation achieves a 20-fold increase. Farrars SSE2 implementation is available as the SSEARCH program in the FASTA sequence comparison package. The SSEARCH is included in the European Bioinformatics Institutes suite of similarity ...

Crickard JB, Moevus CJ, Kwon Y, Sung P, Greene EC. Rad54 Drives ATP Hydrolysis-Dependent DNA Sequence Alignment during Homologous Recombination. Cell. 2020.

0034]FIG. 6 illustrates a flow chart of an exemplary method 100 for aligning template 18 and substrate 12. In a step 102, a field 70 having multiple sub-fields 92 on the edge 74a of substrate 12 may be provided. Alignment system 90 may be configured to be in optical communication with alignment marks 72 of field 70. Alignment marks 72 may be positioned at outer boundary of field 70. Each sub-field 92 may comprise multiple alignment marks 72a. In a step 104, at least one potentially yielding sub-field 92 may be identified. Potentially yielding sub-fields 92 may have one or more potentially yielding dies. In a step 106, alignment measurement system 90 may be re-configured such that alignment measurement units 62 capture alignment marks 72a within potentially yielding sub-field 92 or a combination of one or more potentially yielding sub-fields 92. For example, alignment measurement system 90 may be repositioned to be in optical communication with alignment marks 72a of the potentially yielding ...

Lithographic offset alignment techniques for MOS dynamic RAM memory cell fabrication to enable increased packing density while maintaining the minimum patterned geometry. Technique of cell fabrication involves initial oxidation of P-type silicon, for example, followed by silicon nitride deposition. Thereafter, moats are etched using the composite silicon dioxide-silicon nitride layers, followed by boron deposition or ion implantation in regions of the silicon substrate exposed by the etching treatment. The moats are then filled by oxidation to form a large field deposit of silicon dioxide extending above the level of the oxide layer in the regions where the moats were formed. The remaining composite silicon dioxide-silicon nitride layers are then removed, followed by gate oxidation. A P-type ion implant is provided beneath the thin oxide region between the regions to be overlaid by a polysilicon electrode and the thick field oxide of the succeeding cell. Thereafter, polysilicon is deposited and

AUTOMOTIVE TECHNICIAN / TIRE TECH + ALIGNMENT at RNR TIRE EXPRESS AND CUSTOM WHEELS - Tupelo in Tupelo, MS. The Alignment / Tire & Wheel Technician (tire tech) is responsible for overseeing all activity in the installation shop.The Tire & Wheel Technician ensures that all paperwork related to installs or removals is completed properly, inventory is properly maintained and monitored, and that proper tools and equipment are always in the shop.The Alignment / Tire & Wheel Technician is generally offered as a full time positions and offers benefits plus paid vacation...

Sequence alignment of Yarrowia lipolytica Pex24p with the proteins Yhr150p and Ydr479p encoded by the Saccharomyces cerevisiae genome. Amino acid sequences were

Endothelial cell alignment in the direction of blood flow has been known for many years; recent work indicated that localized activation of Rac1 GTPase at the downstream side of the endothelial cell is a critical event in flow-induced alignment.6 Here we report that localized α4 integrin phosphorylation leads to this localized Rac1 activation and subsequent stress fiber alignment and endothelial cell elongation parallel to the flow direction in response to shear stress. α4 integrins were phosphorylated within 5 minutes of shear stress exposure and phosphorylation occurred predominantly at the downstream edges of the cells. Inhibition of PKA blocked α4 phosphorylation and prevented both localized Rac1 activation and stress fiber alignment in the flow direction. Furthermore, α4 integrins are required for endothelial cell alignment because deletion of α4 or addition of antibodies against α4 inhibited stress fiber alignment. Most importantly, PKA phosphorylation of α4 is involved in alignment ...

Macromolecular assemblies play an important role in almost all cellular processes. However, despite several large-scale studies, our current knowledge about protein complexes is still quite limited, thus advocating the use of in silico predictions to gather information on complex composition in model organisms. Since protein-protein interactions present certain constraints on the functional divergence of macromolecular assemblies during evolution, it is possible to predict complexes based on orthology data. Here, we show that incorporating interaction information through network alignment significantly increases the precision of orthology-based complex prediction. Moreover, we performed a large-scale in silico screen for protein complexes in human, yeast and fly, through the alignment of hundreds of known complexes to whole organism interactomes. Systematic comparison of the resulting network alignments to all complexes currently known in those species revealed many conserved complexes, as well as

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.. ...

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, researchers at the South African National Bioinformatics Institute have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (

A central problem in the bioinformatics of gene regulation is to find the binding sites for regulatory proteins. One of the most promising approaches toward identifying these short and fuzzy sequence patterns is the comparative analysis of orthologous intergenic regions of related species. This analysis is complicated by various factors. First, one needs to take the phylogenetic relationship between the species into account in order to distinguish conservation that is due to the occurrence of functional sites from spurious conservation that is due to evolutionary proximity. Second, one has to deal with the complexities of multiple alignments of orthologous intergenic regions, and one has to consider the possibility that functional sites may occur outside of conserved segments. Here we present a new motif sampling algorithm, PhyloGibbs, that runs on arbitrary collections of multiple local sequence alignments of orthologous sequences. The algorithm searches over all ways in which an arbitrary number of

An optical alignment system for aligning a film cassette carrying grid cassette with an x-ray source of a portable x-ray apparatus. To facilitate accurate alignment of the central x-ray beam of the x-ray source of a portable x-ray apparatus with a focused grid in a clinical setting, the present invention uses a light projector and a reflector device. The light projector is substantially fixed relative to the x-ray source and projects a spot or line of light on the surface of the grid cassette. The reflector device, which can be temporarily or permanently fixed to the grid cassette, includes a reflector surface and an image surface. Images of the incident light spot or line and of the reflected light spot or line are formed on the image surface, and the distance between the images indicates the magnitude of angulation alignment error between the grid cassette and the x-ray source. When beam alignment is accurate, the incident light spot or line and reflected light spot or line will be substantially

Supplementary MaterialsFigure S1: Sequence alignment of the spicing variants induced by the zdia2 sMO. from dorsal order PF-4136309 view (A and order PF-4136309 C) and side view (B and D).(3.22 MB TIF) pone.0003439.s002.tif (3.0M) GUID:?E5FCF276-E9BE-4CCB-B4D6-652824A35BE2 Physique S3: Knockdown of interferes with protrusion formation at marginal deep cells during epiboly cell movement. Embryos injected with stdMO (ACC) or sMO (DCF) and GFP-GAP43 mRNA were observed under confocal microscope at the 50% epiboly to shield stage. Movies with 15 frame per sec were recorded and selected snapshots from one of the stdMO-injected and sMO-injected embryos movies with DIC channel (A and D), GFP channel (B and E) and overlap of two channels (C and F) are showed here. Blebbing cell processes are indicated by arrowheads.(3.18 MB TIF) pone.0003439.s003.tif (3.0M) GUID:?87348770-49E4-49AF-932E-006929AF4281 Physique S4: Knockdown of inhibit actin condensation at the YSL. Embryos injected with 8 ng stdMO (A and ...

PyMod 2.0 is a PyMOL plugin, designed to act as simple and intuitive interface between PyMOL and several bioinformatics tools (i.e., PSI-BLAST, Clustal Omega, MUSCLE, CAMPO, PSIPRED, and MODELLER). The current PyMod release, PyMod 2.0, has been extended with a rich set of functionalities that substantially improve it over its predecessor (PyMod 1.0), particularly in its ability to build homology models through the popular MODELLER package. Starting from the amino acid sequence of a target protein, users may take advantage of PyMod 2.0 to carry out the three steps of the homology modeling process (that is, template searching, target-template sequence alignment and model building) in order to build a 3D atomic model of a target protein (or protein complex). Additionally, PyMod 2.0 may also be used outside the homology modeling context, in order to extend PyMOL with numerous types of functionalities. Sequence similarity searches, multiple sequence-structure alignments and evolutionary conservation ...

The RNA shapes studio comprises four RNA secondary structure prediction tools, which make heavy use of shape abstraction. An abstract shape is a mathematically well defined coarse grained view of an RNA structure, supporting the user to focus only on interesting structural features. RNAshapes and pKiss operate on single sequence inputs. Their counterparts RNAalishapes and pAliKiss take an multiple sequence alignment as input. RNAshapes and RNAalishapes predict purely nested secondary structures. pKiss and pAliKiss additionally consider H-type pseudoknots and kissing hairpins. KnotInFrame - KnotInFrame is a pipeline to predict ribosomal -1 frameshift sites with a simple pseudoknot as secondary structure in DNA and RNA sequences.. pAliKiss - pAliKiss is a tool for secondary structure prediction including kissing hairpin motifs.. pKiss - pKiss is a tool for secondary structure prediction including kissing hairpin motifs.. pknotsRG - RNA folding and thermodynamic matching RapidShapes - Computes a ...

PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing.. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that faciliates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit, which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and ...

PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing.. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that faciliates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit, which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and ...

0036] At step 2 of FIG. 1, the replicate sequence reads are aligned to correlate each call in each read to a given position in the target sequence, thereby generating a multiple sequence alignment (MSA). In a general sense, an MSA is a representation of a common alignment of several (e.g., more than two) overlapping sequences, which provides more information than a single pairwise alignment. For example, a single polypeptide sequence can be matched against an entire polypeptide sequence family, or a single nucleotide sequence can be matched against a set of homologous sequences from different chromosomes and/or individuals in a population. The MSA is useful in various aspects, including aiding in the discovery of evolutionary relationships between different individuals (e.g., organisms, species, strains, etc.), and identification of key regions of such sequences (e.g., highly conserved regions are usually key functional regions and potentially prime targets for drug development; polypeptide ...

What youre looking for when you are measuring is to see whether the distances are … Then, reposition the strings and recheck the alignment of the toe. In order to navigate out of this carousel please use your … Safety issues aside, there are a few statistics that you might want to keep at the back of your mind as you continue to drive your … Before making an adjustment, make sure to review your cars exact measurements. Sep 13, 2020 #1 I spent some time reading the different threads going back a few years regarding DIY alignments. Next Last. DIY wheel camber alignment regulation is not difficult as it may seem at first. Youll still want to get a computerized alignment if this happens, but get to a shop - and avoid personal injury and vehicle damage - by using these DIY alignment tips. That is why, you should approach responsibly to the wheel camber alignment. Having done the measurements, Ive put both front wheels around 0.1 degrees toe in … Its no news that the wrong-regulated wheel ...

Looking for online definition of beam alignment in the Medical Dictionary? beam alignment explanation free. What is beam alignment? Meaning of beam alignment medical term. What does beam alignment mean?

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. We developed a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. Our implementation is freely available at http://bioinfo.lifl.fr/path/ .

ProMSED2: Protein Multiple Sequence EDitor-2 for Win 3.11/95 State Research Center of Virology an Biotechnology Vector Institute of Molecular Biology Koltsovo, Novosibirsk Region, 633159 Russia ProMSED2, Windows application for both automatic and manual DNA and protein sequence alignment, editing, comparison and analysis is available from EBI software library: ftp://ftp.ebi.ac.uk/pub/software/dos/promsed/prsed2_.exe (as self-extracted archive). If you have access to e-mail only, the program can be obtained via e-mail by sending the following message: To: BITFTP at pucc.Princeton.EDU From: YOUR E-MAIL ADDRESS ftp ftp.ebi.ac.uk uuencode user anonymous cd pub/software/dos/promsed get prsed2_.exe quit Server will return you uuencoded program in several files. Running UUDECODE youll get the archive with the program. DESCRIPTION ProMSED2 is the enhancement of ProMSED made according to users remarks and suggestions. The program reads main sequence formats and performs automatic alignments, ...

Abstract: For protein sequence datasets, unlabeled data has greatly outpaced labeled data due to the high cost of wet-lab characterization. Recent deep-learning approaches to protein prediction have shown that pre-training on unlabeled data can yield useful representations for downstream tasks. However, the optimal pre-training strategy remains an open question. Instead of strictly borrowing from natural language processing (NLP) in the form of masked or autoregressive language modeling, we introduce a new pre-training task: directly predicting protein profiles derived from multiple sequence alignments. Using a set of five, standardized downstream tasks for protein models, we demonstrate that our pre-training task along with a multi-task objective outperforms masked language modeling alone on all five tasks. Our results suggest that protein sequence models may benefit from leveraging biologically-inspired inductive biases that go beyond existing language modeling techniques in NLP ...

Immunoglobulin alignments in Sulfolobus tokodaii str. 7. Alignments can be refined by adding alignments from other genomes, adding your own sequences and/or aligning to other models from the same superfamily. The display of alignments can also be customised.

Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization, and protein functionality. We present SEDB, the Structural Exon Database, with a web interface, an application which allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms ...

Term] id: EDAM:0002078 name: Sequence range format namespace: format def: Format used to specify range(s) of sequence positions. subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0001017 ! Sequence range [Term] id: EDAM:0002571 name: Raw sequence format namespace: format def: Format of a raw molecular sequence (i.e. the alphabet used). subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000848 ! Raw sequence [Term] id: EDAM:0001921 name: Alignment format namespace: format def: Data format for molecular sequence alignment information. subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0001919 name: Sequence record format namespace: format def: Data format for a molecular sequence record. subset: format is_a: EDAM:0002350 ! Format (typed) relationship: is_format_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0002057 name: Sequence trace format namespace: ...

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel

Background Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. Methodology/Principal Findings We describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs breakpoint score, which facilitates accurate detection of rearrangement breakpoints when genomes have unequal gene content. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying ...

In this book the author makes an ``effort to render both mathematical equations and biology to numbers. Following this premise, he works out a lot of illustrative examples to make biologists understand the mathematics and computational scientists understand the biology of a wide range of problems in bioinformatics.. In the first chapters the author introduces the mathematics of string-matching algorithms in FASTA and BLAST and explains pairwise and multiple sequence alignments. There are sections about aligning rRNA genes with the constraint of secondary structure and about alignments of nucleotide sequences against amino acid sequences. A whole chapter is devoted to contig assembly algorithms. Several chapters deal with gene and motif predictions. Position weight matrices, perceptrons and hidden Markov models are introduced. The Gibbs sampler is used to identify regulatory sequences in DNA or functional motifs in proteins.. The book also covers the analysis of proteins and proteomes, e.g., ...

We address the problem of Phylogenetic Placement, in which the objective is to insert short molecular sequences (called query sequences) into an existing phylogenetic tree and alignment on full-length sequences for the same gene. Phylogenetic placement has the potential to provide information beyond pure species identification (i.e., the association of metagenomic reads to existing species), because it can also give in- formation about the evolutionary relationships between these query sequences and to known species. Ap proaches for phylogenetic placement have been developed that operate in two steps: first, an alignment is esti mated for each query sequence to the alignment of the full-length sequences, and then that alignment is used to find the optimal location in the phylogenetic tree for the query sequence. Recent methods of this type include HMMALIGN+EPA, HMMALIGN+pplacer, and PaPaRa+EPA.We report on a study evaluating phylogenetic placement methods on biological and simulated data. This ...

This directory contains alignments of the following assemblies: - target/reference: Human (hg19, Feb. 2009 (GRCh37/hg19), GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)) - query: (araMac1, , ) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - hg19.araMac1.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - hg19.araMac1.net.gz: net file that describes rearrangements between the species and the best match to any part of the Human genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - axtNet/*.hg19.araMac1.net.axt.gz: chained and netted alignments, i.e. the best chains in the Human genome, with gaps in the best chains filled in by next-best chains where possible. The axt format is described in http://genome.ucsc.edu/goldenPath/help/axt.html . The hg19 and araMac1 assemblies were aligned by the blastz alignment ...

The Profile Hidden Markov Model (PHMM) can be poor at capturing dependency between observations because of the statistical assumptions it makes. To overcome this limitation, the dependency between residues in a multiple sequence alignment (MSA) which is the representative of a PHMM can be combined with the PHMM. Based on the fact that sequences appearing in the final MSA are written based on their similarity; the one-by-one dependency between corresponding amino acids of two current sequences can be append to PHMM. This perspective makes it possible to consider a generalization of PHMM. For estimating the parameters of modified PHMM (emission and transition probabilities), we introduce new forward and backward algorithms. For this purpose, we consider the generalized PHMM as a Bayesian Network (BN). A Bayesian network is a specific type of graphical model which is a directed acyclic graph (DAG). The performance of modified PHMM is discussed by applying it to the twenty protein families in Pfam ...

Domains, evolutionarily conserved units of proteins, are widely used to classify protein sequences and infer protein function. Often, two or more overlapping domain models match a region of a protein sequence. Therefore, procedures are required to choose appropriate domain annotations for the protein. Here, we propose a method for assigning NCBI-curated domains from the Curated Domain Database (CDD) that takes into account the organization of the domains into hierarchies of homologous domain models. Our analysis of alignment scores from NCBI-curated domain assignments suggests that identifying the correct model among closely related models is more difficult than choosing between non-overlapping domain models. We find that simple heuristics based on sorting scores and domain-specific thresholds are effective at reducing classification error. In fact, in our test set, the heuristics result in almost 90% of current misclassifications due to missing domain subfamilies being replaced by more generic domain

Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The ini …

Another direction that is being taken is to adapt primary sequence alignment methods to consider secondary and tertiary structure. There are a number of features of proteins integral to their function and interaction with other proteins that are not determined by amino acid sequence alone. Many proteins share functional properties despite vast sequence differences because of the shapes that they fold into. One method of simultaneously quantifying and visualizing these relationships is using a protein structure space map. [¹] Roughly speaking, a Protein structure space map is the result of scoring how well known proteins match, structurally. That score is used as a directional distance used to position families of proteins in relation to each other on a set of axes, closer if they are more similar, distantly if they are more dissimilar. Anyone can look at the structure space map and immediately judge how similar two proteins or protein families are by their proximity on the map.. There are a ...

Using a multiple alignment of 175 cytochrome P450 (CYP) family 2 sequences, 20 conserved sequence motifs (CSMs) were identified with the program PCPMer. substrates 7-methoxy-4-(trifluoromethyl)coumarin (7-MFC), 7-ethoxy-4-(trifluoromethyl)coumarin (7-EFC), 7-benzyloxy-4-(trifluoromethyl)coumarin (7-BFC), and testosterone and with the inhibitors 4-(4-chlorophenyl)imidazole (4-CPI) and bifonazole (BIF). Compared with the template and K186A, the mutants R187A, R187K, F188A, Y190A, and D192A showed 2-fold altered substrate specificity, metabolism of bupropion (14 -17). Mutations in all the variants are located in non-active site regions. Two of the non-synonymous changes in particular, Q172H and K262R, are found in multiple haplotypes. Frequencies of the three most common variants range from 14 to 49% for Q172H, 17 to 63% for K262R, and 0 to 14% for R487C depending on the ethnicity of the population analyzed (17). At present, the structural basis for the altered function of P450 2B6 variants or for ...

While brightfield images (e.g. stained in H&E) are the primary choice for observing the morphology of the tissue, fluorescence images are better for the visualization of the cellular characteristics. Digital multiplexing of brightfield and fluorescence images can combine the benefits of both worlds while maintaining the individual characteristics of each of the modalities. Many digital pathology scanners available today are equipped to scan images in both brightfield and fluorescence mode. When using both modes for a tissue sample, adjoined sections are typically prepared and scanned separately and the resulting whole slide images (WSIs) need to be reviewed or analyzed individually. Aligning images from multiple modalities can help aggregating information from consecutive sections stained in histochemical and fluorescent dyes, e.g. protein expression and gene amplification by aligning immunohistochemical (IHC) markers with fluorescence in-situ hybridization (FISH). The aligned images can then be ...

Analysis of the human exome and transcriptome by next-generation sequencing has improved the state of cancer research, because it allows for the detection of variant alleles that may drive tumorigenesis. The consequence of variants introduced post-transcriptionally in the transcriptome through RNA editing is that function and regulation of mRNA and miRNA can be affected, resulting in nonfunctional proteins or proteins with different functions than those intended in the genome sequence. Despite the extensive studies, many functional variants introduced through RNA editing are likely to have been missed because they occur at a low frequency, or in a tissue- or tumor-specific manner. My research is focused on the application of RNA2DNAlign, a new sequence alignment program developed by the Horvath lab, to detect or identify novel variants through the comparison of the normal and tumor exome and transcriptome sequences from the same individual. We downloaded human genome and transcriptome datasets from

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Metagenome sequencing efforts have provided a large pool of billions of genes for identifying enzymes with desirable biochemical traits. However, homology search with billions of genes in a rapidly growing database has become increasingly computationally impractical. Here we present our pilot efforts to develop a novel alignment-free algorithm for homology search. Specifically, we represent individual proteins as feature vectors that denote the presence or absence of short kmers in the protein sequence. Similarity between feature vectors is then computed using the Tanimoto score, a distance metric that can be rapidly computed on bit string representations of feature vectors. Preliminary results indicate good correlation with optimal alignment algorithms (Spearman r of 0.87, ~;;1,000,000 proteins from Pfam), as well as with heuristic algorithms such as BLAST (Spearman r of 0.86, ~;;1,000,000 proteins). Furthermore, a prototype of FASTERp implemented in Python runs approximately four times faster ...

The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in ...