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Showing 12 records out of 12 total

Categories: genomics, (similarity search), evolutionary biology - Software type(s): CLI - tool
BUSCO (Benchmarking Universal Single-Copy Orthologs) provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Homology detection & structure prediction by HMM-HMM comparison
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem.
Categories: proteomics, (protein modifications), genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website, GUI - tool
MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
Categories: genomics, (characterisation/annotation) - Software type(s): website - tool
C++ program for HMM models
Categories: proteomics, (protein structure), structure analysis - Software type(s): website, CLI - tool
predicting coiled-coils in protein sequences
Categories: genomics, (sequence alignment, similarity search), systems biology - Software type(s): website, CLI, GUI - tool
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
Categories: proteomics, (protein structure) - Software type(s): website - tool
As with Phyre, the new system is designed around the idea that you have a protein sequence/gene and want to predict its three-dimensional (3D) structure. Whereas Phyre used a profile-profile alignment algorithm, Phyre2 uses the alignment of hidden Markov models via HHsearch to significantly improve accuracy of alignment and detection rate.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The Sulfinator is a software tool able to predict tyrosine sulfation sites in protein sequences. It employs four different Hidden Markov Models that were built to recognise sulfated tyrosine residues located N-terminally, within sequence windows of more than 25 amino acids and C-terminally, as well as sulfated tyrosines clustered within 25 amino acid windows, respectively. All four HMMs contain the distilled information from one multiple sequence alignment.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Use the SUPERFAMILY database of structural and functional annotation to provide structural (and hence implied functional) assignments to protein sequences primarily at the SCOP superfamily level. A superfamily contains all proteins for which there is structural evidence of a common evolutionary ancestor. This service offers sophisticated and expertly chosen remote homology detection.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
TMHMM is a membrane protein topology prediction method based on a hidden Markov model (HMM). It predicts transmembrane helices in proteins.
Categories: genomics, (sequence alignment), population genetics - Software type(s): CLI - tool
V-pipe is a bioinformatics pipeline for the analysis of next-generation sequencing (NGS) data derived from intra-host viral populations.