Software & Servers
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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.
The toolkit includes, among others: NucleotideBLAST, ProteinBLAST, PSI-BLAST, HMMER3, HHsenser; ClustalW, MUSCLE, Mafft, ProbCons; HHrep, PCOILS, REPPER; Quick2D, HHBlits, HHpred, Modeller; CLANS, ANCESCON, PHYLIP; Reformat, RetrieveSeq.
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HHblits
HHblits is the first iterative method based on the pairwise comparison of profile Hidden Markov Models. In benchmarks it achieves better runtimes than other iterative sequence search methods such as PSI-BLAST or HMMER3 by using a fast prefilter based on profile-profile comparison. Furthermore, HHblits greatly improves upon PSI-BLAST and HMMER3 in terms of sensitivity/selectivity and alignment quality.
The software is part of the bioinformatics toolkit, but can also be downloaded here
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HHpred
Sensitive protein homology detection and structure prediction by HMM-HMM-comparison.
The software is part of the bioinformatics toolkit, but can also be downloaded here
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CS-BLAST
Search with an amino acid sequence against protein databases for locally similar sequences.
The software is part of the bioinformatics toolkit, but can also be downloaded here
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HHomp
Sensitive protein homology detection and classification of outer membrane proteins (OMP) by HMM-HMM-comparison.
The software is part of the bioinformatics toolkit, but can also be downloaded here
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HHrepid
HHrepID, a method for the de novo identification of repeats in protein sequences.