Multiple alignment sequence analysis rna. Medical search. Frequent questions

Using whole-genome quantitative gene expression as a model, here we study how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed in different environments (25 °C and 18 °C). We find a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. (nature.com)
We present a detailed sequence analysis of the 10 formins (ForA to J) identified in the genome of the social amoeba Dictyostelium discoideum . (biomedcentral.com)
We performed whole-genome (WG) de novo sequencing and complete assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk in Korea. (biomedcentral.com)
Moreover, comparative genome analysis of S. fibuligera ATCC 36309, an isolate from chalky rye bread in Germany, revealed that an interchromosomal translocation occurred in the KPH12 genome before the generation of the KJJ81 hybrid genome. (biomedcentral.com)
The completely sequenced S. fibuligera genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of S. fibuligera in the degradation of fermentation mash. (biomedcentral.com)
They are classified into at least three species, HRV-A, HRV-B and HRV-C, which are characterized by sequencing the 5′ untranslated region (UTR) or the VP4/VP2 region of the genome. (plos.org)
Availability http://carnot.utmb.edu/flavitrack Get in touch with ude.bmtu@niehcshc Supplementary details http://carnot.utmb.edu/flavitrack/B1S1.html 1 Launch Flaviviruses (FV) (+)-strand RNA infections in the same genus seeing that hepaci- and pestiviruses are in charge of many emerging individual encephalitic and hemorrhagic illnesses (Barrett and Higgs 2007 The ～10.5 kb genome encodes an individual polyprotein that's cleaved into 10 viral proteins (Fig. 1). (bioskinrevive.com)
The database includes all publicly obtainable full-genome flavivirus sequences and access to series analysis equipment. (bioskinrevive.com)
"Identifying All of Cancer's Manifestations through Integrated Pan Cancer Analysis" Dr. Josh Stuart presented the recent work of The Pan-Cancer Initiative of The Cancer Genome Atlas (TCGA) Research Network, including the analysis of thousands of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels in order to uncover data-driven tumor subtypes. (biomedcentral.com)
For each clinical sample, raw RNA-seq reads were aligned and mapped to the Ensembl GRCh37 human reference genome and assembled using Tophat v2.0.9 resulting in BAM files for each of 59 samples. (nih.gov)
Starting in the 90s, and the human genome project, genomic and mRNA sequences started to become more common in patents. (questel.com)
In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1. (researchsquare.com)
The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. (researchsquare.com)
F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level. (researchsquare.com)
Our comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control. (researchsquare.com)
Advances in whole-genome sequencing technologies have enabled numerous key discoveries. (researchsquare.com)
This is due to our limited access to genome sequences from uncultivated organisms, which are estimated to account for 99% in prokaryotes ( 11 ). (scienceintheclassroom.org)
We used a genome-wide analysis which not only examined differential gene expression levels but could also detect differences in splice isoform usage. (jneurosci.org)
With the application of single cell genome and metagenome sequencing and assembly, the number of phyla in Archaea domain has increased to more than twenty, and these phyla clustered to Euryarchaota and three superphyla-TACK, DPANN, and Asgard [ 15 ]. (biomedcentral.com)
However, single-cell genome and metagenome sequencing have shown limited capacity to discover microbial dark matter because massive data are needed for metagenome assembly and binning. (biomedcentral.com)
Potentially, this step would map most of the reads to a genome, and the remaining "non-mapped" group would be small enough to be subjected to more thorough analysis. (softberry.com)
Transomics pipeline - The pipeline will include the following key components: ReadsMap tools for alignment of RNA-Seq reads to genome, Fgenesh++R identification of alternative transcripts gene prediction tolls, and ExpLevel tool for measuring expression levels of predicted transcript isoforms. (softberry.com)
The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online), using potential mature miRNA sequences as input. (g6g-softwaredirectory.com)
After searching the genome for the provided mature sequences, these hits are extended and classified taking into account major structural properties of known miRNA precursors. (g6g-softwaredirectory.com)
Isolation and Whole-Genome Sequencing of Environmental Campylobacter. (cdc.gov)
Purification of Cyclospora cayetanensis oocysts obtained from human stool specimens for whole genome sequencing. (cdc.gov)
Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. (cdc.gov)
Transposable elements refer to DNA sequences capable of moving from one part of the genome to another. (lu.se)

In eukaryotic cells, chromatin comprises a complex consisting of DNA, RNA, and proteins where covalent modifications correlate with regulation of gene expression [ 1 ]. (biomedcentral.com)
The first three RNAs identified - messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA) were associated with the translation of RNA to proteins - protein synthesis. (biomedcentral.com)
While DNA is known to carry genetic information from one generation to the next, and proteins are capable of forming three-dimensional structures that catalyze chemical reactions, the function of RNA was perceived as the carrier of the information to code for amino acids in a protein, serve as a scaffold for proteins in the ribosome, and attach amino acids to the growing protein chain during protein synthesis. (biomedcentral.com)
RNA is capable of forming complex three-dimensional structure like proteins. (biomedcentral.com)
Different primary structures (or sequences) can form the same higher-order structure for different RNAs and proteins [ 5 ]. (biomedcentral.com)
DNA, RNA sequences as well as proteins have been disclosed in patents since the 60s and a few even before that. (questel.com)
MicroRNAs display exquisite stability in serum or plasma because they are packaged in membrane-encapsulated vesicles or protected by RNA-binding proteins. (gene-quantification.com)

First, there is a common language to describe DNA/RNA and amino acid sequences, entirely independent from the native language the patent is written in. (questel.com)
PhyML - PhyML is a software product that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. (g6g-softwaredirectory.com)

In bioinformatics, Stemloc is an open source software for multiple RNA sequence alignment and RNA structure prediction based on probabilistic models of RNA structure known as Pair stochastic context-free grammars (also probabilistic context-free grammars). (wikipedia.org)
The initial goal of Stemloc was to reduce the time and space cost of simultaneous alignment and structure prediction of two RNA sequences by using a stochastic context-free grammar (SCFG) scoring scheme and by implementing constrained versions of the Sankoff Algorithm. (wikipedia.org)
The combination of mass data analysis and SVM-based feature selection makes our approach a promising method for shape and structure prediction. (biomedcentral.com)
With advances in sequencing technologies and structure prediction, more pseudoknot structures are expected to be disclosed. (biomedcentral.com)
Is the Subject Area "RNA structure prediction" applicable to this article? (plos.org)
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. (g6g-softwaredirectory.com)
Areas covered include sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)

Next, mRNA libraries were prepared from total RNA from lysed cells and subjected to RNAseq on an Illumina Novaseq. (cdc.gov)
MicroRNAs are small, non-coding RNA molecules that can complementarily bind to the mRNA 3'-UTR region to regulate the gene expression by transcriptional repression or induction of mRNA degradation. (gene-quantification.com)
As a method for characterizing global changes in transcription, RNA-Seq is an attractive option because of the ability to quantify differences in mRNA abundance in response to various treatments and diseases, as well as to detect alternative splice variants and novel transcripts[ 1 ]. (biomedcentral.com)

In this 35-minute webinar, learn to perform NGS sequence assembly and alignment for multiple genomes, exomes, and RNA-Seq samples from a desktop or laptop computer. (dnastar.com)
Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages ( 12 - 14 ) and the discovery of a previously unknown reassignment of TGA opal stop codons to glycine ( 4 , 5 , 14 ). (scienceintheclassroom.org)
To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber , TGA opal , and TAA ochre codons in assembled metagenomes and metatranscriptomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of viral sequences ( Fig. 1A ) ( 15 ). (scienceintheclassroom.org)
Furthermore, the manufacturers provide precomputed mappings of all miRBase miRNA sequences across 46 Ensembl genomes and 21 Ensembl Metazoa genomes. (g6g-softwaredirectory.com)
The provided input sequences are scanned against selected genomes using the Bowtie algorithm, which is designed for efficient short sequence matching. (g6g-softwaredirectory.com)

The analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the realizations that 1) RNA is implicated in many more functions within the cell, and 2) the analysis of ribosomal RNA sequences is revealing more about the microbial ecology within all biological and environmental systems. (biomedcentral.com)
By fingerprinting small subunit (SSU) ribosomal RNA (rRNA) sequences, Woese classified all life into three domains: Eukarya, Bacteria, and Archaea [ 5 ]. (biomedcentral.com)

In addition, the use of bacterial 16S rRNA sequencing in the identification of the microbiome in many different environmental systems creates a need for rapid and highly accurate alignment of bacterial 16S rRNA sequences. (biomedcentral.com)
Primer binding regions of universal primer 8F/Arch21F for bacteria or archaea were used for primer evaluation of SSU rRNA sequences in meta-transcriptomic datasets. (biomedcentral.com)
Using this method, we identified unclassified SSU rRNA sequences that were not matched with universal primer 8F and Arch21F. (biomedcentral.com)
A new group within the Asgard superphylum was amplified by the newly designed specific primer based on these unclassified SSU rRNA sequences by using mudflat samples. (biomedcentral.com)

This comparative method is now widely used in the study for many RNAs, and is the cornerstone for the computational analysis of the deluge of nucleic acid sequences that are determined with next-generation sequencing methodology. (biomedcentral.com)
Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples. (cdc.gov)

The phylogenetic trees based on the 16S rRNA gene sequences showed that strain 1KV19 T was associated with the genus Lutibacter and had the highest 16S rRNA gene sequence similarity to Lutibacter oceani 325-5 T with 98.1 % similarity. (microbiologyresearch.org)
Similarity and phylogenetic analysis were used to confirm their novel status. (biomedcentral.com)
The manufacturers focus on the task of mapping an identified miRNA in one species to others using both sequence similarity and RNA secondary structure. (g6g-softwaredirectory.com)

RNA sequencing (RNA-Seq) is emerging as a highly accurate method to quantify transcript abundance. (biomedcentral.com)

The pipeline job result is an optimal (most full with maximal homology) coverage of every "target" sequences by fragments of the "query" set ones. (softberry.com)

GenomeMatch - a tool to compare genomic sequences. (softberry.com)

In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. (frontiersin.org)
However, analyses of the large data sets obtained by sequencing the entire transcriptome of organisms have generally been performed by bioinformatics specialists. (biomedcentral.com)
Analysis of transcriptome sequence data with estimates of gene expression level and identification of gene structure of expressed splice variant. (softberry.com)

To establish the relationship between formins of Dictyostelium and other organisms we constructed a phylogenetic tree based on the alignment of FH2 domains. (biomedcentral.com)
Multiple dimensions of cross-indexed information are contained within the relational database - rCAD, including sequence alignments, the NCBI phylogenetic tree, and comparative secondary structure information for each aligned sequence. (biomedcentral.com)

Precalculated sequence alignments integrated with the Jalview (Clamp et al . (bioskinrevive.com)
Primary components evaluation (PCA) of aligned sequences (using Jalview) enables fast derivation of phylogenetic viral groupings most certainly relating to vector (Fig. 2). (bioskinrevive.com)
This includes the generation and display of Maximum Likelihood phylogenetic trees (PhyML & PhyloWidget), Multiple sequence alignments (MUSCLE & Jalview) and RNA Structural logos (RNALogo). (g6g-softwaredirectory.com)

Multi-sample BAM QC analysis of a H2AX ChiP-seq experiment in human cells comparing four different conditions (Koeppel This mode allows computation of metrics specific to RNA-seq data, including per-transcript coverage, junction sequence distribution, genomic localization of reads, 5C3 bias and consistency of the library protocol. (buyresearchchemicalss.net)

18 ), respectively, and the sequences were downloaded from the European Molecular Biology Laboratory/GenBank/DNA Data Bank of Japan. (cdc.gov)
stemloc nanos-tiny.rna -nf -1 -na -1 Another feature of Stemloc is its ability to parameterize probabilistic models like stochastic context-free grammars from data. (wikipedia.org)
To determine the KIF12 major splice variant, RNA-sequencing data and sequence alignments of KIF12 homologues were used. (nottingham.ac.uk)
In this tutorial participants will learn about biological data analysis with R and Unix/Linux tools. (r-bloggers.com)
We begin with an introduction to bioinformatics and omics data analysis, and conclude with the walkthrough of a simple bioinformatics workflow for aligning transcriptomic sequences with genomic data. (r-bloggers.com)
Be able to use bioinformatics software tools to prepare omics data for analysis. (r-bloggers.com)
It is a computational field that involves the analysis of complex omics data. (r-bloggers.com)
This commonly includes DNA, RNA, or protein sequence data. (r-bloggers.com)
The following graphic depicts a typical workflow for preparing, analyzing, and visualizing results from transcriptomic RNA sequencing data. (r-bloggers.com)
In this lesson you will gain experience in performing omics data analysis by working through part of a bioinformatics pipeline for analyzing gene expression data. (r-bloggers.com)
As a first step, we will begin with collecting some data for analysis. (r-bloggers.com)
Several existing NGS QC software tools including RNA-seq QC (DeLuca 2012), a toolkit for QC of HTS alignment data. (buyresearchchemicalss.net)
Counts are usually applicable for analysis of differential gene expression from RNA-seq data (Anders 2013). (buyresearchchemicalss.net)
To assist data analysis of the huge alignments each series has been by hand assigned a distinctive identifier a 'permit dish' which concisely shows important info about the disease. (bioskinrevive.com)
In this task view, we focus on the most-important CRAN packages dedicated to omics data analysis including those related to annotation and databases. (osuosl.org)
VAM proposes a gene set testing method that is better designed than standard ones to handle single-cell RNA-seq data. (osuosl.org)
tmod provides functions for gene set enrichment analysis in transcriptomic and metabolic profiling data. (osuosl.org)
CePa aims to find significant pathways through network topology information and pathfindR (accompanied by the data package pathfindR.data ) and netgsa also use network information for enrichment analysis. (osuosl.org)
SlaPMEG performs pathway enrichment analysis for longitudinal omics data. (osuosl.org)
The accurate and rapid alignment of these RNA sequences is essential to decipher the maximum amount of information from this data. (biomedcentral.com)
The assembly was characterized, including analyses of the genomic structure, with the aim of providing data to support the discovery of beneficial or harmful genes and to improve our understanding of the molecular pathogenesis. (researchsquare.com)
Because of the high variability between methods for determining differential expression of RNA-Seq data, we suggest using several bioinformatics tools, as outlined here, to ensure that a conservative list of differentially expressed genes is obtained. (biomedcentral.com)
In an effort to familiarize the bench scientist with the post-sequencing analysis of RNA-Seq data (phase 5), we have developed an analysis strategy based on currently available bioinformatics tools. (biomedcentral.com)
Dozens new algorithms have been developed for next-generation sequencing (NGS) data processing. (softberry.com)
RNASeq reads clustering program that assembles the RNA-Seq data into unique sequences of transcripts generates full-length transcripts for a set of alternatively spliced isoforms. (softberry.com)
The program demonstrates Sensitivity 0.97 and Specificity 0.96 in identifying known RNA transcripts on test data. (softberry.com)
Threats to timely sharing of pathogen sequence data. (cdc.gov)
Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus. (cdc.gov)
Analysis of DENV sequence data facilitates rapid disease USA). (cdc.gov)
Sequence data obtained were deposited in GenBank tracking and vector control. (cdc.gov)
During my Ph.D. studies, my focus has been analyzing sequencing data in relation to transposable elements. (lu.se)
I have been mainly involved in the data analysis and interpretation of this data, working closely with biologists who conduct experiments in the lab. (lu.se)
My focus has been on the data analysis side of things, employing different computational methods to deal with mapping ambiguity and adapting new technologies such as single-cell RNA sequencing to better understand three families of transposable elements. (lu.se)

At the second step, we use a modified variant of our EST_MAP program to align these "non-mapped" reads using splice site matrices and producing very accurate alignment with gaps. (softberry.com)

Two computer systems that utilize the Gutell lab's RNA Comparative Analysis Database (rCAD) were developed to align sequences to an existing template alignment available at the Gutell lab's Comparative RNA Web (CRW) Site. (biomedcentral.com)

Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. (plos.org)
A summary of mutants and variant sequences tabulated relating to produced strains area of mutations related altered phenotypes as well as the references for every mutation continues to be contained in Flavitrack. (bioskinrevive.com)
A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. (researchsquare.com)
DOI: http://dx.doi.org/10.3201/eid1811.120014 between multiple circulating strains and serotypes. (cdc.gov)

Neighbor-joining phylogenetic trees for viral protein (VP) 7 G1, G2, G3, and G9 genotypes of hospitalized children in Israel, including sequences recovered from archived rotavirus dipsticks. (cdc.gov)

Using a -1 will unlimited the number of folds and alignments sampled, thus using -1 for both parameters will run the Sankoff algorithm on the input dataset. (wikipedia.org)
This resource, combining a unique new dataset and novel application of analysis methods to multiple relevant datasets, identifies numerous potential drug targets for manipulating circuit function, reveals neuron subtype-specific roles for disease-linked genes, and is useful for understanding gene expression changes observed in human patient brains. (jneurosci.org)
When comparing statistical tools, the negative binomial distribution-based methods, edgeR and DESeq, respectively identified 11,995 and 11,317 differentially expressed genes from an RNA-seq dataset generated from soybean leaf tissue grown in elevated O 3 . (biomedcentral.com)

When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. (plos.org)

Finally, we highlight several aspects of RNA-Seq analysis that have the potential to lead to misleading conclusions and discuss options to minimize these pitfalls. (biomedcentral.com)

In proof theory they offer a deep analysis of structural rules, demystifying some of their properties, and putting them into context. (ne.jp)

2004 multiple alignment editor are provided for those polyproteins in Flavitrack (presently 544 sequences) a synopsis subset of 49 specific FV and one which combines all of the FV pestivirus and hepacivirus polyproteins in the NCBI (923 sequences). (bioskinrevive.com)

Through deep metagenome sequencing of ultra-small microbes, Anantharaman et al. (biomedcentral.com)

Upon analysis of the non-significant genes, several limitations of these analytic tools were revealed, including evidence for overly stringent parameters for determining statistical significance of differentially expressed genes as well as increased type II error for high abundance transcripts. (biomedcentral.com)
Compared to microarray techniques, RNA-Seq eliminates the need for prior species-specific sequence information and overcomes the limitation of detecting low abundance transcripts. (biomedcentral.com)

The simultaneous assessment of multiple samples allows examination of consistency between samples and visual detection of outliers (Fig. 1A). (buyresearchchemicalss.net)
The mode was completely redesigned to allow processing of multiple samples. (buyresearchchemicalss.net)
Tmem44 Similar to the previous version, the mode estimates the saturation of sequencing depth, read count densities, correlation of samples and distribution of counts among classes of selected features (Supplementary Figs. S1CS4). (buyresearchchemicalss.net)
B) Map showing the locations of 82 environmental samples around the globe together with nine sample sites (derived from 212 samples) of the human body for which recoded sequences have been identified. (scienceintheclassroom.org)
No degradation was observed in any of the samples and staining of the 26S rRNA band was more intense compared to the 18S rRNA band, indicating that high quality RNA had been isolated. (biomedcentral.com)
Following library preparation and sequencing-by-synthesis, analysis of the raw reads determined that all six samples had a median quality score (QS) of 34 (Table 1 ). (biomedcentral.com)
The haemagglutinin (HA) segments of A(H1N1)pdm09 from both real-time RT-PCR positive and negative samples were isolated and sequenced. (who.int)
Sequencing was conducted on 23 influenza (H1N1)pdm09 isolates that were recovered from positive samples. (who.int)
How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis. (cdc.gov)

Scasa, an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. (ne.jp)
Sequences were preprocessed with adapter trimming and alignment-free quantification with Kallisto using Ensembl v96 transcriptomes. (cdc.gov)
We also conclude that despite these analytical limitations, RNA-Seq provides highly accurate transcript abundance quantification that is comparable to qRT-PCR. (biomedcentral.com)

Full-envelope protein sequences for each serotype their initial consultation or are still in transit during their were aligned by using the multiple alignment tool of viremic phase. (cdc.gov)

chekiangensis from leaves and bulbs, and viruses were identified using a phylogenetic analysis and BLAST search for sequence. (ppjonline.org)

Paired-end, strand specific sequencing for total RNA was performed on Illumina HiSeq 2500 with 100 bp read lengths. (nih.gov)

Our knowledge of the diversity of genetic codes and their use by viruses and their hosts is primarily derived from the analysis of cultivated organisms. (scienceintheclassroom.org)
The primer and probe sets in the HA gene were checked for mismatches, and phylogenetic analyses were performed to determine the molecular epidemiology of these viruses. (who.int)

Stemloc attempts to simultaneously predict and align the structure of RNA sequences with an improved time and space cost compared to previous methods with the same motive. (wikipedia.org)
liger and GSA also propose methods for gene set enrichment analysis. (osuosl.org)
Methods We performed whole exome sequencing in a consanguineous family with heterotaxia. (bmj.com)
Therefore, universal primer-independent sequencing library construction methods are needed. (biomedcentral.com)

In Qualimap 2, we provide new analysis capabilities that allow multi-sample comparison of sequencing datasets. (buyresearchchemicalss.net)
To estimate the variability between analyzed datasets, Qualimap performs a principal component analysis based on specific features derived from the alignment, including coverage, GC content, insert size and mapping quality (Fig. 1B). (buyresearchchemicalss.net)
We also apply our analysis to two other relevant datasets for comparison, and provide a searchable website for convenient access to the resource. (jneurosci.org)
The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets. (biomedcentral.com)
I have used various RNA and DNA-based technologies, including both short-read and long-read sequencing techniques, and worked to integrate these datasets, including bulk and single-cell datasets. (lu.se)

As a result, biologists studying an array of model and non-model organisms are beginning to utilize RNA-Seq analysis with ever growing frequency[ 3 - 7 ]. (biomedcentral.com)

Fold: RNA folding is the process by which an RNA molecule acquires secondary structure through intra-molecular interactions. (wikipedia.org)

In addition, there was no evidence that genomic DNA was co-purified during RNA extraction. (biomedcentral.com)

Fold envelope: The set of candidate folds to be considered in the algorithm Alignment envelope: The set of candidate alignments to be considered in the algorithm A previously developed algorithm by David Sankoff in 1985 uses dynamic programming to simultaneously align and predict multiple RNA structures. (wikipedia.org)
Stemloc uses alignment envelopes and fold envelopes to simultaneously constrain both the alignment and the secondary structures of the sequences being compared. (wikipedia.org)
Fold envelopes can be used to "prune" the search over secondary structures and determine the subsequences of two RNA sequences that can be considered in the algorithm. (wikipedia.org)
Fold envelopes are pre-calculated for each sequence individually, and alignment envelopes are pre-calculated by comparing the two sequences while ignoring secondary structures. (wikipedia.org)
For example, the using the "-fast" command below will only consider the 100 best RNA structures rather than analyzing all possible folds. (wikipedia.org)
Extensive analysis of RNA properties based on SVM allows us to identify important properties of sequences and structures related to their shapes. (biomedcentral.com)
Many types of ncRNAs perform their functions through both their sequences and secondary structures, which are defined by the interacting base pairs. (biomedcentral.com)
As knowing the secondary structure provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs, deriving the secondary structures of ncRNAs remains an important research topic in RNA informatics. (biomedcentral.com)
The identification and characterization of macromolecular sequences and their higher-order structures have utilized a very important principle in molecular and evolutionary biology. (biomedcentral.com)

gprofiler2 provides an interface for g:Profiler (including functional enrichment analysis, identifier conversion, or orthology across species). (osuosl.org)
16S rRNA gene-based analyses showed that less than 10 species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. (biomedcentral.com)
The user then decides which species to map these sequences against. (g6g-softwaredirectory.com)

The GenBank accession numbers for all sequences in this figure appear in the online Appendix Table (Table A). Scale bars indicate percent of nucleotide substitutions per site. (cdc.gov)

Sample input shown below: stemloc --local dynalign.trna The "--local" command analyzes the file in local alignment mode. (wikipedia.org)

The accuracies of the two CRWAlign programs were compared with the best template-based rRNA alignment programs and the best de-novo alignment programs. (biomedcentral.com)

While the size of the folding space of an RNA sequence increases exponentially with the sequence length [ 10 ], many possible folding only differ in the details of the loop and helix regions and hence have the same abstract shape. (biomedcentral.com)

These thresholds have been selected according to an empirical analysis of true and shuffled miRNA sequences. (g6g-softwaredirectory.com)

It shows the sequence names, the co-ordinates of the matches, the alignment, the consensus primary sequence, the secondary structure of each sequence, the consensus secondary structure, and the log-odds score of the alignment in bits. (wikipedia.org)
More specifically, each sequence can be pre-folded individually in O ( L 3 ) {\displaystyle O(L^{3})} time and pre-aligned, ignoring secondary structure in O ( L 2 ) {\displaystyle O(L^{2})} time. (wikipedia.org)
The second program, CRWAlign-2 creates a profile based on phylogenetic, secondary structure, and sequence information. (biomedcentral.com)

https://www.biorxiv.org/content/10.1101/2021.11.23.469039v1.full.pdf a new algorithm for aligning both reads in a pair simultaneously by fuzzily intersecting the sets of candidate alignment locations for each read. (ne.jp)
Of these reads, ~10-15% aligned to multiple genomic loci. (nih.gov)
Furthermore, targeted forward primers were designed based on SSU rRNA reads from unclassified groups unmatched with the universal primer 8F/Arch21F, and these primers were used to amplify nearly full-length special SSU rRNA gene sequences along with universal reverse primer 1492R. (biomedcentral.com)
The OligoZip algorithm is enhanced by iterative module of accounting paired reads and adding a new procedure of restoration of repeated sequences in assembled scaffolds. (softberry.com)
On initial stage we map "exonic" reads that demonstrate high-quality, non-interrupted alignment to a genomic sequence. (softberry.com)

Several downstream analyses are performed and their utility in applied ecology, evolutionary biology and molecular biology research will be discussed with guest lecturers. (lu.se)

The system is supplied with a set of input sequences corresponding to mature miRNA sequences. (g6g-softwaredirectory.com)

After multiple failed attempts to express and purify rsKif12, sequence analysis showed rsKif12 lacks nucleotide-binding motifs conserved across the kinesin superfamily. (nottingham.ac.uk)
search for RNA and RNA motifs in genomic databases. (universiteitleiden.nl)

Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments are shared and have similar effects, analysis of the environment-specific eQTLs reveals enrichment of binding sites for two transcription factors. (nature.com)
This analysis reveals numerous examples of neuron subtype-specific isoform usage with functional importance, identifies potential drug targets, and provides insight into the neuron subtypes involved in psychiatric disease. (jneurosci.org)

"Single-Cell Analysis of Tumor Heterogeneity" Intratumor heterogeneity is a critical impediment to improving prognosis of many types of cancer such as breast and prostate cancer. (biomedcentral.com)

Anatomy7

Organisms12

Diseases3

Chemicals and Drugs86

Analytical, Diagnostic and Therapeutic Techniques and Equipment40

Phenomena and Processes94

Disciplines and Occupations3

Information Science26

Health Care14

Genome28

Proteins7

Amino acid sequences2

Prediction7

MRNA3

Genomes5

Ribosomal2

RRNA sequences4

Nucleic2

Similarity3

Quantify transcript1

Homology1

Genomic sequences1

Transcriptome3

Phylogenetic tree2

Jalview3

Metrics1

Data33

Splice1

RCAD1

Strains4

Viral1

Dataset3

Comparative1

Conclusions1

Structural1

NCBI1

Metagenome1

Transcripts2

Samples9

Quantification3

Protein sequences1

Identified using a phylog1

Illumina HiSeq1

Viruses2

Methods4

Datasets5

Organisms1

Molecule1

Extraction1

Structures9

Species3

GenBank1

Trna1

Novo1

Abstract1

Empirical analysis1

Secondary3

Reads5

Evolutionary1

MiRNA1

Motifs2

Reveals2

Single-cell1