Protein domain prediction software tools | Sequence analysis
Protein domains are conserved and distinct protein sequences and structures that can function independently of the rest of the protein. Protein domains often have specific function or interaction and contribute to the activity of the protein. Protein domain prediction tools use protein sequence and biochemical properties such as hydrophobicity combined with algorithm to predict and identify domains.
Finds evolutionarily related proteins and/or domains, close and remote homologs. HMMER is based on profile hidden Markov models (HMMs) and gathers four algorithms: phmmer, hmmscan, hmmsearch, and jackhmmer. It assists users in the detection of protein sequence conservation, function, and evolution. This tool can be useful for functional annotations. It offers a solution to make research on protein sequence databases.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Aims to detect protein matches against signatures from the PROSITE database, a resource that contains large collection of biologically meaningful signatures. ScanProsite is a web application that offers several online functionalities: (1) detection of intra-domain biological features, (2) a new graphical result representation and (3) an interactive result viewer.
Aggregates a number of protein annotation tools and provides services or software to allow users to perform truly scalable biological analyses. PSIPRED offers to the user the possibility to choose the method wanted to conduct the analysis. It proposes the following sequence and structure annotation methods: PSIPRED, GenTHREADER, pGenTHREADER, pDomTHREADER, MEMSAT-SVM/MEMSAT3, MEMPACK, BioSerf, MetSite, HSPred, DISOPRED2, DomPred and FFPred. The tool permits to select any number of appropriate simultaneous analyses across all the applicable methods and easily explore results.
Combines transmembrane topology and signal peptide predictions. Phobius provides an easy and accurate mean to predict signal peptides and transmembrane topology from an amino acid sequence. Phobius makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions.
Scans sequences against InterPro's signatures. InterProScan allows users to characterize a nucleotide or protein function by matching it with models from several different databases and to obtain a better overview of their results. The software performs relatively small numbers of sequences in a single analysis, including the ability to parallelize search jobs to minimize wall-clock time.
Permits users to detail and annotate probesets on Affymetrix GeneChip microarrays. NetAffx allows users to search for probesets matching specified criteria such as annotation terms, as well as to identify any probesets relevant to a user-specified DNA sequence. It furnishes protein annotations derived by sequence homology, using the GRAPA method on collections of hidden Markov models (HMMs), representing well-characterized protein families.