Welcome to the Bioinformatics Toolkit
The Bioinformatics Toolkit is a platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality.
Most frequently used tools
HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. HHpred builds a
profile HMM from a query sequence and compares it with a database of HMMs representing annotated protein
families (e.g. PFAM, SMART, CDD, COGs, KOGs) or domains with known structure (PDB, SCOP). The output is a
list of closest homologs with alignments.
HHblits Remote homology detection method based on iterative HMM-HMM comparison.
Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets,
coiled coils, transmembrane helices and disorder regions.
Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2.
Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints.
Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils
and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation.
PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive.
PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search.
After each successive round the search alignment is updated.
To find a tool not listed here, choose the appropriate section tab above, or look for the tool in the Quickfinder on the top right corner.
Job submission
Each tool has a separate input page with a web form in which the user can input sequence data, upload sequence files, and specify options. All tools that take alignments as input accept the most widely used formats (FASTA, CLUSTAL, Stockholm and A3M). You may also choose your own job-names to organize your work. Snail symbols inside the submit buttons inform you about tools that typically run for more than 10 minutes.
Job management
Located on the left of the screen is a sidebar pane that holds a status
and section-coded list of all recent jobs in the current session. You can click
on previously submitted jobs to check their status and view their results.
In general a session will last until the web browser is closed. However,
because of different session implementations by the various browser types, jobs
may occasionally disappear from the joblist. Therefore, noting down the job ids is
recommended. Anonymous job results are stored two
weeks, whereas jobs of logged-in users are stored at least two months.
Interconnectivity
Most of the tools in the Toolkit are interconnected, allowing job results of one tool to be forwarded as input to others. For example, you could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool.
User databases
You may upload customized databases which are then accessible throughout the whole toolkit (upload once, use many times).