• The algorithms developed include Gibbs sampler, artificial neural networks, position specific scoring matrix (PSSM) construction, sequence clustering, hidden Markov models, and sequence profile-based alignment methods. (dtu.dk)
  • PSI-BLAST first performs a BLASTP search to collect information that it then uses to produce a Position-Specific-Scoring-Matrix ( PSSM ). (nih.gov)
  • A PSSM for a query of length N is an N x 20 matrix. (nih.gov)
  • Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. (biomedcentral.com)
  • A Position-Specific Sequence Matrix (PSSM) has been pre-built for each type and is used as a low threshold first pass filter for region detection using the Smith-Waterman algorithm to find local alignments. (labkey.org)
  • To generate an alignment for variable regions, the PSSM-matched sub-sequence is aligned to both germline V-segments and J-segments and these results are combined to synthesize an alignment for the entire variable region. (labkey.org)
  • Use a PSSM for the region type to find local alignments in the query ii. (labkey.org)
  • Generate a refined region alignment for the PSSM alignment i. (labkey.org)
  • In this paper, we report a novel computational approach combining fuzzy local ternary pattern (FLTP), Position-Specific Scoring Matrix (PSSM), and rotation forest (RF) to identify DTIs. (imrpress.com)
  • Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
  • Probabilistic methods try to maximize the relative entropy or Kullback-Leibler divergence [ 7 ], obtained from the construction of a Position Specific Score Matrix (PSSM). (biomedcentral.com)
  • In the DMEC, we evolved a population of PSSM matrices using a canonical evolutionary algorithm and a greedy mutation operator. (biomedcentral.com)
  • Similarity scores are taken from the position specific similarity matrix (PSSM) generated by PSI-BLAST. (cchmc.org)
  • Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments. (wikipedia.org)
  • Sequences that score significantly better to the profile-HMM compared to a null model are considered to be homologous to the sequences that were used to construct the profile-HMM. (wikipedia.org)
  • This work is based upon earlier publication showing a significant acceleration of the Smith-Waterman algorithm for aligning two sequences. (wikipedia.org)
  • Profile HMMs turn a multiple sequence alignment into a position-specific scoring system, which can be used to align sequences and search databases for remotely homologous sequences. (wikipedia.org)
  • This tool compares nucleotide or protein sequences to genomic sequence databases and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST) algorithm. (nih.gov)
  • The DendroSSR employs a technique containing multiple phases beginning with, detecting SSRs, computing SSRs similarities, sequences alignment, building a distance matrix based on SSRs similarity and sequences alignments, and then hierarchical clustering, and presenting the findings in a dendrogram. (bvsalud.org)
  • Therefore, establishing a distance matrix that is formed of addition of SSRs similarity across sequences to the traditional sequence alignment helps the process substantially and resolves the connections of complex species on phylogenetic trees. (bvsalud.org)
  • If instead BLAST started out by attempting to align two sequences over their entire lengths (known as a global alignment), fewer similarities would be detected, especially with respect to domains and motifs. (nih.gov)
  • The megaBLAST nucleotide-nucleotide search, optimized for very similar sequences (in the same or in closely related species), first looks for an exact match of 28 bases, and then attempts to extend that initial match into a full alignment ( 3 , 4 ). (nih.gov)
  • Each row corresponds to a specific residue and describes the probability of related sequences having that residue at that position. (nih.gov)
  • When the biologists get an unknown sequence, in general they would compare this unknown sequence (denoted as query sequence) with the known database of sequences (denoted as database sequences) to find the similarity scores and then identify the evolutionary relationships among them. (hindawi.com)
  • Needleman and Wunsch [ 1 ] proposed a dynamic programming method (abbreviated to NW algorithm) to solve the global alignment problem between two sequences in 1970. (hindawi.com)
  • The comparison uses a scoring matrix (a derivative of the Dayhoff evolutionary distances table or PAM matrix) and an existing optimal alignment of two or more similar protein sequences. (ucdavis.edu)
  • The group or 'family' of similar sequences are first aligned together to create a multiple sequence alignment . (ucdavis.edu)
  • The similarity of new sequences to an existing profile can be tested by comparing each new sequence to the profile with the same algorithm used to make optimal alignments. (ucdavis.edu)
  • Alignment algorithms find alignments between two sequences that maximize the number of matches and minimize the number of gaps. (ucdavis.edu)
  • The profile contains a consensus sequence for the display of alignments of other sequences to the profile. (ucdavis.edu)
  • 61-66 (1988)) have aligned the sequences from a number of known protein structural motifs and calculated a group of profiles from these alignments. (ucdavis.edu)
  • Since the profile represents the alignment of a number of known sequences, it contains information that defines where the family of sequences is conserved and where it is variable. (ucdavis.edu)
  • These are available as position-specific score matrices (PSSMs) for fast identification of conserved domains in protein sequences via RPS-BLAST. (readthedocs.io)
  • Compare sequences using pairwise or multiple sequence alignment methods. (mathworks.com)
  • Extract some sequences from GenBank®, find open reading frames (ORFs), and then align the sequences using global and local alignment algorithms. (mathworks.com)
  • The common pairwise comparison methods are usually not sensitive and specific enough for analyzing distantly related sequences. (mathworks.com)
  • HMM profiles use a position-specific scoring system to capture information about the degree of conservation at various positions in the multiple alignment of these sequences. (mathworks.com)
  • This can be justified because gaps that arise from the comparison of closely related sequences should not be moved because of later alignment with more distantly related sequences. (uni-bielefeld.de)
  • At each alignment stage, you align two groups of already aligned sequences. (uni-bielefeld.de)
  • Then, these scores are used to calculate a "guide tree" or dendrogram, which will tell the multiple alignment stage in which order to align the sequences for the final multiple alignment. (uni-bielefeld.de)
  • This topic describes the methodology developed by Just-Evotec Biologics, Inc for the structural alignment and classification of full sequences from antibodies and antibody-like structures using the Antibody Structural Numbering system (ASN). (labkey.org)
  • The CoreAb Java library (developed at Just - Evotec Biologics) contains algorithms for the classification and alignment of antibodies and antibody-like sequences. (labkey.org)
  • The germline sequences are stored as ASN-aligned so that the resulting region alignments are also ASN-aligned. (labkey.org)
  • Definitions Pairwise alignment The process of lining up two or more sequences to achieve maximal levels of identity (and conservation, in the case of amino acid sequences) for the purpose of assessing the degree of similarity and the possibility of homology. (slideserve.com)
  • where While these strings aren't biologically valid DNA sequences, they are the strings you can use to debug your algorithm. (pekarenklasok.sk)
  • Filtering can eliminate statistically significant but biologically uninteresting reports from the blast output (e.g., hits against common acidic-, basic- or proline-rich regions), leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences. (gu.se)
  • MFMD can find and classify overrepresented patterns in DNA sequences and predict their respective initial positions. (biomedcentral.com)
  • To make these guidelines easily accessible to anyone planning a CRISPR genome editing experiment, we built a new website ( http://crispor.org ) that predicts off-targets and helps select and clone efficient guide sequences for more than 120 genomes using different Cas9 proteins and the eight efficiency scoring systems evaluated here. (biomedcentral.com)
  • Unless the multiple sequence alignment (MSA) for a given protein is provided by the user, alignments are generated on the server side using three iterations of PSI-BLAST with the profile-inclusion threshold of expect (e)-value = 0.001 and the number of aligned sequences 5000. (cchmc.org)
  • They capitalise on the fact that certain positions in a sequence alignment tend to have biases in which residues are most likely to occur, and are likely to differ in their probability of containing an insertion or a deletion. (wikipedia.org)
  • The probability of emitting a particular residue is determined largely by the frequency at which that residue has been observed in that column of the alignment, but also incorporates prior information on patterns of residues that tend to co-occur in the same columns of sequence alignments. (wikipedia.org)
  • Multiple I state can occur consecutively, corresponding to multiple residues between consensus columns in an alignment. (wikipedia.org)
  • Since the table on which the profile is based is usually the Dayhoff evolutionary distance table, the consensus residue is the residue that has the smallest evolutionary distance from all of the residues in that position of the alignment rather than simply the most frequent residue at that position. (ucdavis.edu)
  • 18 The human immune system started generating antibodies specific to residues outside RBD even at the earlier stage of the pandemic. (biorxiv.org)
  • This is done using a dynamic programming algorithm where one allows the residues that occur in every sequence at each alignment position to contribute to the alignment score. (uni-bielefeld.de)
  • Structure-based sequence alignments were generated and the residues in the helix-helix interfaces were analyzed. (biomedcentral.com)
  • A subgroup of rice and maize NIPs has small residues in three of the four positions in the ar/R tetrad, resulting in a wider constriction. (biomedcentral.com)
  • The Smith-Waterman (abbreviated to SW) algorithm, which was proposed by Smith and Waterman [ 2 ] in 1981, is designed to find the optimal local alignment, and it is enhanced by Gotoh [ 3 ] in 1982. (hindawi.com)
  • A search of the database using a profile as a probe involves making an optimal alignment of every sequence in the database to the profile and listing the alignments for which the alignment score is outstanding. (ucdavis.edu)
  • The alignment of a sequence to a profile is inherently more sensitive since the whole surface of comparison can be used to find the optimal alignment. (ucdavis.edu)
  • At each alignment stage, we use the algorithm of Myers and Miller (1988) for the optimal alignments. (uni-bielefeld.de)
  • Optimal string alignment distance can be computed using a straightforward extension of the Wagner-Fischer dynamic programming algorithm that computes Levenshtein distance. (pekarenklasok.sk)
  • Note that for the optimal string alignment distance, the triangle inequality does not hold: OSA(CA,AC) + OSA(AC,ABC) (pekarenklasok.sk)
  • To help you verify the correctness of your algorithm, the optimal alignment of these two strings should be -1 (your code should compute that result for … the popular Levenshtein algorithm (Levenshtein, 1965) which uses insertions (alignments of a seg-mentagainstagap),deletions(alignmentsofagap against a segment) and substitutions (alignments of two segments) often form the basis of deter-mining the distance between two strings. (pekarenklasok.sk)
  • Capturing this information gives them a better ability to detect true homologs than traditional BLAST-based approaches, which penalise substitutions, insertions and deletions equally, regardless of where in an alignment they occur. (wikipedia.org)
  • COBALT is a protein multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. (nih.gov)
  • CD-Search uses RPS-BLAST (Reverse Position-Specific BLAST) to compare a query sequence against position-specific score matrices that have been prepared from conserved domain alignments present in the Conserved Domain Database (CDD). (nih.gov)
  • There are many ways of performing a sequence similarity search, but probably the most popular method is the "Basic Local Alignment Search Tool" ( BLAST ) ( 1 , 2 ). (nih.gov)
  • As the name implies, BLAST performs "local" alignments. (nih.gov)
  • The BLAST algorithm is tuned to find these domains or shorter stretches of sequence similarity. (nih.gov)
  • BLASTP performs protein-protein sequence comparison, and its algorithm is the basis of many other types of BLAST searches such as BLASTX and TBLASTN . (nih.gov)
  • RPSBLAST (Reverse-Position-Specific BLAST ) can very quickly search a protein query against a database of PSSMs that were usually produced by PSI-BLAST . (nih.gov)
  • Profile-HMMs are constructed from a multiple sequence alignment in the HMMER package using the hmmbuild program. (wikipedia.org)
  • Profile HMMs center around a linear set of match (M) states, with one state corresponding to each consensus column in a sequence alignment. (wikipedia.org)
  • NCBIfam is a collection of protein families, featuring curated multiple sequence alignments, hidden Markov models (HMMs) and annotation, which provides a tool for identifying functionally related proteins based on sequence homology. (readthedocs.io)
  • Sometimes sequence alignments alone may not give adequate information to generate a phylogenetic tree to resolve complicated species relationships. (bvsalud.org)
  • Each local alignment is then refined by a more careful alignment comparison to the germline gene segments from species specified in the detection settings. (labkey.org)
  • The serine at position 1199 is well conserved among the RP1L1 family in other species. (molvis.org)
  • This track shows the multiple alignments of 26 Drosophila species and measurements of evolutionary conservation using two methods ( phastCons and phyloP ) from the PHAST package . (wustl.edu)
  • Scoring matrices were referred to as symbol comparison tables in previous releases of the Accelrys GCG (GCG)) Gaps are given penalties in the same units as the values in the scoring matrix. (ucdavis.edu)
  • The position-specific gap coefficients penalize gaps in conserved regions more heavily than gaps in more variable regions. (ucdavis.edu)
  • The positions of gaps that are generated in early alignments remain through later stages. (uni-bielefeld.de)
  • Alignment gaps usually result from small-scale genome rearrangements, such as InDels. (pekarenklasok.sk)
  • N eff is the effective sum of weights of alignments where both positions are not gaps. (cchmc.org)
  • w sl is a weighted count of state s, which is equal to 1 for non-weighted scores, 1-(percent of sequence identity) or 1-(percent of gaps) of the alignment l for weighting by sequence dissimilarity or alignment gapping, respectively, and w a ph for weighting by phylogeny. (cchmc.org)
  • arginine and lysine) receive a high score, two dissimilar amino … Saul B. Needleman and Christian D. Wunsch devised a dynamic programming algorithm to the problem and got it published in 1970. (pekarenklasok.sk)
  • Therefore, SSRs may support the knowledge gathered from sequence alignments by providing more information on genetic variation and even evolutionary relationships. (bvsalud.org)
  • 14 ] mentioned that the matK region was preferred as a barcode candidate because of high evolutionary rate, low transition/transversion rate, and inter-specific divergence. (biomedcentral.com)
  • We have developed in previous work two approaches called Discovery Motifs by Evolutionary Computation (DMEC) [ 17 ] and Discovery Motifs by Memetic Algorithms (DMMA) [ 18 ]. (biomedcentral.com)
  • DMMA is an evolution of DMEC where we have some heuristics along with traditional evolutionary algorithm. (biomedcentral.com)
  • For most of these approaches, the emphasis is on the application of canonical evolutionary algorithms to solve biosequence problems. (biomedcentral.com)
  • A profile HMM takes this modelling of sequence alignments further by modelling insertions and deletions, using I and D states, respectively. (wikipedia.org)
  • M, I and D states are connected by state transition probabilities, which also vary by position in the sequence alignment, to reflect the different frequencies of insertions and deletions across sequence alignments. (wikipedia.org)
  • Finally, we performed a comparative assessment of these signatures with the existing methods including BLASTn, Support Vector Machines (SVM), Jrip-RIPPER, J48 (C4.5 algorithm), and the Naïve Bayes (NB) methods against NCBI-GenBank matK dataset. (biomedcentral.com)
  • specifying the MATRIX directive in BLASTN requests returns an error response. (gu.se)
  • This string of match states emitting amino acids at particular frequencies are analogous to position specific score matrices or weight matrices. (wikipedia.org)
  • These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function, as well as inference of amino acids important for functional specificity. (readthedocs.io)
  • All metrics based on frequencies are computed using four states as possible combinations of amino acids at two positions (i and j), where each amino acid is either equal (X) or not equal (!X) to the one in the query sequence. (cchmc.org)
  • Scores for each metric are organized in symmetrical matrices with the main diagonal presenting plain or weighted frequencies, as defined above, of each individual residue for MI-and χ2-based metrics, and the individual Shannon entropies using 20 states (20 amino acids) for S-based metric. (cchmc.org)
  • Pairwise alignments in the 1950s. (slideserve.com)
  • The pairwise sequence alignments were generated using LAST . (wustl.edu)
  • The server computes pairwise coevolution scores using three metrics: Mutual Information, Chi-square Statistic, and Pearson correlation. (cchmc.org)
  • This study introduces a new method to construct phylogenetic trees by combining both of the Simple Sequence Repeats (SSRs) and sequence alignments. (bvsalud.org)
  • Phylogenetic analysis indicated a highly dynamic evolution of all three lipid-modifying enzymes in land plants, with many clade-specific duplications or losses and massive diversification of the C2-PLD family. (frontiersin.org)
  • Harnessing machine learning to guide phylogenetic-tree search algorithms. (tau.ac.il)
  • This algorithm is a very memory efficient variation of Gotoh's algorithm (Gotoh, 1982). (uni-bielefeld.de)
  • The local alignment approach also means that an mRNA can be aligned with a piece of genomic DNA , as is frequently required in genome assembly and analysis. (nih.gov)
  • Transcription factors are specific proteins that bind to distinct sites on the genome. (biomedcentral.com)
  • Gene regulation in the human genome is controlled by distal enhancers that activate specific nearby promoters 1 . (nature.com)
  • Often, though, distinct searches infer multiple topologies with large log-likelihood score differences or yield topologically highly distinct, yet almost equally likely, trees. (bvsalud.org)
  • Easy multiple sequence alignments (MSAs) exhibit a single likelihood peak on their likelihood surface, associated with a single tree topology to which most, if not all, independent searches rapidly converge. (bvsalud.org)
  • The information in the multiple sequence alignment is then represented quantitatively as a table of position-specific symbol comparison values and gap penalties. (ucdavis.edu)
  • Each row in the profile corresponds to a position in the original multiple sequence alignment. (ucdavis.edu)
  • CDD is a protein annotation resource that consists of a collection of annotated multiple sequence alignment models for ancient domains and full-length proteins. (readthedocs.io)
  • Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. (readthedocs.io)
  • HMM profile analysis can be used for multiple sequence alignment, for database searching, to analyze sequence composition and pattern segmentation, and to predict protein structure and locate genes by predicting open reading frames. (mathworks.com)
  • The multiple sequence alignments were generated using the tools developed by UCSC and the Miller lab at the Penn State University Center for Comparative Genomics and Bioinformatics. (wustl.edu)
  • 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. (wustl.edu)
  • Dozens of genes had multiple DMRs that were often seemingly positioned to regulate specific splice variants. (biomedcentral.com)
  • Scasa splits the equivalence class output by cell and applies the AEM algorithm to multiple cells. (ne.jp)
  • The adaptation of correspondence analysis for to the integration of multiple tables is similar to the method for single tables with additional matrix concatenation operations. (ne.jp)
  • Multiple sequence alignment as a sequence-to-sequence learning problem. (tau.ac.il)
  • My strong interest for characterization and development of algorithms used in bioinformatics has led me to conduct a course specialized in this area. (dtu.dk)
  • The course, Algorithm in Bioinformatics (27623) is running each autumn starting 2008. (dtu.dk)
  • The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. (hindawi.com)
  • In bioinformatics, the sequence alignment has become one of the most important issues. (hindawi.com)
  • The algorithm selects only those substitutions that are consistent with the alignment … i b Experience. (pekarenklasok.sk)
  • EvoRator2: predicting site-specific amino acid substitutions based on protein structural information using deep learning Journal of Molecular Biology: 435(14):168155. (tau.ac.il)
  • We here present Memetic Framework for Motif Discovery (MFMD), an algorithm that uses semi-greedy constructive heuristics as a local optimizer. (biomedcentral.com)
  • In addition, we have included the Variable Neighborhood Search (VNS) algorithm [ 16 ], that is a greedy local search method that explores the solution space through systematic exchanges of increasingly distant neighborhood structures. (biomedcentral.com)
  • SFLD (Structure-Function Linkage Database) is a hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities. (readthedocs.io)
  • In this paper, we introduce MFMD a memetic algorithm [ 14 ] whose goal is to solve De novo motif discovery problem. (biomedcentral.com)
  • This communication system is based on specific lipids as messengers and enzymes responsible for their production and degradation. (frontiersin.org)
  • Phosphoinositides (PPIs) together with various kinases and phosphatases were described as specific lipids and enzymes with signaling functions earlier ( Martin, 1998 ). (frontiersin.org)
  • In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). (wustl.edu)
  • To this end, we collect data from eight SpCas9 off-target studies and compare them with the sites predicted by popular algorithms. (biomedcentral.com)
  • We propose to model coordination between two different DSMs trained on two distinct corpora as dimensionality selection over a dense matrix obtained via Singular Value Decomposition This approximates an ad-hoc coordination scenario between two speakers as the attempt to align their similarity ratings on a set of word pairs. (frontiersin.org)
  • Though the NW and SW algorithms guarantee the maximal sensitivity for the alignment, the cost is still expensive, especially for the computation time. (hindawi.com)
  • The best alignment is then simply defined as the alignment for which the sum of the scoring matrix values minus the gap penalties is maximal. (ucdavis.edu)
  • The best alignments of a sequence to a profile are found by aligning the symbols of the sequence to the profile in such a way that the sum of the profile comparison values minus the gap penalties is maximal. (ucdavis.edu)
  • and 2) their geometric structure allows for exploiting alignment-based similarity metrics to measure inter-subject alignment over an entire semantic space, rather than a set of limited entries. (frontiersin.org)
  • Typically, it works by computing TF metrics for each sentence in the given matrix. (911weknow.com)
  • Coevolution scores are computed from the MSA using three different covariance metrics: mutual information ( MI , Eq. 1), chi-square statistic ( χ 2 , Eq. 2), and Pearson correlation ( r , Eq. 3). (cchmc.org)
  • Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity. (readthedocs.io)
  • Cutoff score for reporting high-scoring segment pairs. (gu.se)
  • To generate the initial classic networks, we demonstrated that changes in reported cases before the current position in the segment average aciphex for sale tracking vector. (margottriesthegoodlife.com)
  • The molecular substrates underlying this integration are complex and not well understood [ 6 ], but rapid responses to changing circumstances depend on flexible brain function, i.e. neural plasticity, which in turn is supported by context-specific patterns of gene transcription [ 7 ]. (biomedcentral.com)
  • An in-house algorithm predicts and ranks expert authors for each gene based on the data within FlyBase and extracts their email addresses from papers that we have curated. (stanford.edu)
  • We also evaluate on-target efficiency prediction algorithms against available datasets. (biomedcentral.com)
  • Moreover, we find that for the problem of the prediction of the disulfide connectivity it is possible to increase the predicting performance by initializing the Radial Basis Function kernels with a k-mean clustering algorithm. (scitevents.org)
  • Definitions Conservation Changes at a specific position of an amino acid or (less commonly, DNA) sequence that preserve the physico-chemical properties of the original residue. (slideserve.com)
  • Specify an alternate scoring matrix for BLASTP, BLASTX, TBLASTN and TBLASTX. (gu.se)
  • 2. The alignment produces a 1Typical units in a set are n-grams of a string, which pre-serves local features of a string and tolerates discrepancies. (pekarenklasok.sk)
  • Sequence alignments are also used for non-biological se… Local alignment requires that we find only the most aligned substring between the two strings. (pekarenklasok.sk)
  • He is a member of the Intelligent Sensing and Communications (ISC) Group and his major research interests are in mathematical theory and algorithms for data analysis. (ncl.ac.uk)
  • Also, an option for computing conservation scores based on the Joint Shannon Entropy is provided. (cchmc.org)
  • Each metric, in turn, is computed using four weighting schemes: weighted by sequence dissimilarity or sequence gapping in the alignment (Eqs. (cchmc.org)
  • To demonstrate the utility of these markers, we provide haplotype networks, DNA alignments, and summary statistics regarding the sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA). (mdpi.com)
  • The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1. (wustl.edu)
  • My research in development of novel pattern recognition algorithms aims at developing method that can improve our ability for rational design of vaccines against human and animal infections likeHIV, Tuberculosis, Malaria, and food and mouth disease. (dtu.dk)
  • Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. (hindawi.com)
  • A method that can be used to investigate the significance of sequence alignments. (mathworks.com)
  • The characteristic properties of the images of yeast colonies, as produced by the setup used in the cooperating genetics laboratory, are described, the underlying counting algorithm is reviewed and the performance of the method is evaluated, using a test set of 245 images. (scitevents.org)
  • In this article, we compare existing scoring systems against published datasets and our own experimental data. (biomedcentral.com)
  • In addition, we used a hybridization of the classic genetic algorithm as a global optimizer to refine the solutions initially found. (biomedcentral.com)
  • Find support for a specific problem in the support section of our website. (mdpi.com)
  • Basically, they both find an alignment score. (pekarenklasok.sk)
  • We identify problems in one implementation but found that sequence-based off-target predictions are very reliable, identifying most off-targets with mutation rates superior to 0.1 %, while the number of false positives can be largely reduced with a cutoff on the off-target score. (biomedcentral.com)
  • In 2008, Manavski and Valle [ 16 ] presented the first SW algorithm by CUDA for the protein database search on GPU. (hindawi.com)
  • Ligowski and Rudnicki [ 18 ] also presented another SW algorithm for the protein database search on GPU in 2009. (hindawi.com)