PATOSEQPATOSEQ is a motif search and alignment program [Documentation]. |
Pedro Gonnet and Frédérique Lisacek. Probabilistic alignment of motifs with sequences. Bioinformatics 2002 18: 1091-1101
Contact address: pedro.gonnet@genebio.com
Up-to-date documentation and standalone version
PATOSEQ (PATtern TO SEQuence alignments) is a tool that aligns a motif to a set of amino acid sequences. If only one set is specified (in the left box), the motif will be scanned against this set. If a second set is supplied in the right box, the motif will be optimized in subsequent runs to discriminate between the two sets. Each set may be input in any format by pasting them into the text boxes or by uploading a local file. A predefined set can also be selected, to reproduce the results given in the PATOSEQ article. The default parameters will optimize a motif for the discrimination between B. subtilis lipoproteins and non-lipoproteins, as detailed in the article. Several rounds of optimizations may be necessary to refine the motif as much as possible.