Software & Servers

  • XXmotif server 

    To analyze gene regulatory networks, the DNA/RNA binding affinities of proteins and ncRNAs are critical. Often, these are deduced from sets of sequences enriched in factor binding sites. Binding affinity landscapes can be described by positional weight matrices (PWMs). The XXmotif web server can discover motifs that are enriched in sets of nucleotide sequences provided by the user. XXmotif uses a new approach for finding enriched motifs: It directly optimizes the statistical significance of enrichment for PWMs. It can also score conservation and positional clustering of motifs. In several benchmarks on yeast and metazoan sequences, the underlying XXmotif method showed better sensitivity and produced PWMs of higher quality than state-of-the-art tools.

    The open source XXmotif software can be downloaded here.

     

  • HH-suite software

    The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). It contains HHsearch and HHblits among other programs and utilities. HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous proteins. HHsearch is often used for protein structure prediction to detect homologous templates and to build highly accurate query-template pairwise alignments for homology modeling. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments.

    The open source HH-suite software package can be downloaded here.

     

  • HHblits server

    Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments.

    The HHblits software is part of the open source package HHsuite.

  • HHpred server

    Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. 

  • Bioinformatics toolkit

    The Bioinformatics Toolkit is a web-based platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house in Tubingen and Munich, 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.

     

  • CS-BLAST server

    Search with an amino acid sequence against protein databases for locally similar sequences.

    The software can be downloaded here.

     

  • HHomp server

    Sensitive protein homology detection and classification of outer membrane proteins (OMP) by HMM-HMM-comparison.

    The software can be downloaded here

     

  • HHrepid server

    HHrepID, a method for the de novo identification of repeats in protein sequences.