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Bioinformatics

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Software. This page lists all biological software that has been developed by Ben Stöver and Kai Müller. Note that this list also contains programs which have been replaced by extended projects we started later on. LibrAlign LibrAlign - A GUI library for displaying and editing multiple sequence alignments and attached data TreeGraph 2 TreeGraph 2 is a graphical editor for phylogenetic trees which allows you to apply lots of graphical formats to the elements of your tree. Moreover, it supports several (visible or invisible) annotations (e.g. support values) for every branch or node. These annotations can be imported from Nexus tree files or text files containing data in a table (e.g. exported from a spreadsheet program). SeqState Primer design, sequence statistics, and indel coding according to various schemes PhyDE System-independent editor for DNA and amino acid sequence alignments, designed to assist anybody interested in phylogenetic or other comparative analyses of sequence data TreeGraph IndelCoder.

BIOSERVER home page. PredictProtein - Structure Prediction and Sequence Analysis. GeneMark™ - Free gene prediction software. The GeneMark-P and GeneMark-E algorithms determine protein-coding potentials, the values of a posteriory probability of protein coding in a DNA fragment in six possible reading frames. The six frame GeneMark graph shows details of the protein-coding potential distribution along the sequence. The GeneMark.hmm-P and GeneMark.hmm-E algorithms predict prokaryotic (P) and eukaryotic (E) genes in a sequence as a whole.

The algorithms use the Hidden Markov models reflecting the "grammar" of gene organization. The GeneMark.hmm (P and E) algorithms identify the maximum likely parse of the whole DNA sequence into protein coding genes (with introns in E case) and intergenic regions. * "P" stands for "Prokaryotic" "E" stands for "Eukaryotic" "S" stands for "Self-training" For more information see Background and Publications. Mfold Web Server. Phylogeny.fr: Home. Welcome to the Worldwide Protein Data Bank. InterPro protein sequence analysis & classification. InterPro: protein sequence analysis & classification InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.

Read more about InterPro Documentation About InterPro: core concepts, update frequency, how to cite, team and consortium members. FAQs: what are entry types and why are they important, interpreting results, downloading InterPro? Web services documentation Protein focus The sweetest thing Our sugar consumption has reached to such a level that it carries health risks such as obesity, diabetes. Publications The InterPro protein families database: the classification resource after 15 years Our latest paper describing new developments on the InterPro website (Nucleic Acids Research, Jan 2015). Tools InterProScan Blog. UniProt Knowledgebase: Swiss-Prot and TrEMBL. Genome Browser. Information Génomique et Structurale - CNRS UPR2589. National Center for Biotechnology Information.