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.
Assists users in studying a single structural fold in a single model organism as proof of principle. HHSearch is a sequence-sequence comparison tool used to annotate databases. Profiles are built by using multiple sequence alignments (MSA) of protein families which characterize the probability of the occurrence of an amino acid in a column of a MSA. This software can also be useful for discovering remote homologies.
Predicts 3D structure of a protein sequence. Phyre is a web application that investigates known homologues, builds a hidden Markov model (HMM) of the targeted sequence based on the detected homologues and scans it against a database of HMMs of known protein structures. It also provides advanced features such as a batch submission of a large number of protein sequences for modelling or Phyre Investigator, that allows users to analyze model quality, function and effects of mutations.
A web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. ConSurf combines two independent servers (ConSeq and ConSurf), providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences.
Permit to search sequences against collections of profiles. HMMER hmmscan is a web application. This tool is a simple multiple steps process: (i) user sets the tool input (e.g. sequences, databases...) in FASTA or UniProtKB/Swiss-Prot format, and (ii) user has the possibility to change the default tool parameters and submit the information specified previously in the form to launch the tool on the server.
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin). The package also covers most of the standard sequence analysis tasks such as restriction site searching, translation, pattern searching, comparison, gene finding, and secondary structure prediction, and provides powerful tools for DNA sequence determination.
Assists users with DNA sequence analysis. Sequencher is a graphical application that integrates the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. It can generate unique data visualizations using customized plots and graphs that produces ready-to-print graphs. This model also includes an extensive Sanger analysis features.