IsoSVM - Distinguishing isoforms and paralogs on the protein level

Background: Recent progress in cDNA and EST sequencing is yielding a deluge of sequence data. Like database search results and proteome databases, this data gives rise to inferred protein sequences without ready access to the underlying genomic data. Analysis of this information (e.g. for EST clustering or phylogenetic reconstruction from proteome data) is hampered because it is not known if two protein sequences are isoforms (splice variants) or not (i.e. paralogs/orthologs). However, even without knowing the intron/exon structure, visual analysis of the pattern of similarity across the alignment of the two protein sequences is usually helpful since paralogs and orthologs feature substitutions with respect to each other, as opposed to isoforms, which do not. Results: The IsoSVM tool introduces an automated approach to identifying isoforms on the protein level using a support vector machine (SVM) classifier. Based on three specific features used as input of the SVM classifier, it is p...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Michael Spitzer, Stefan Lorkowski, Paul Cullen, Alexander Sczyrba, Georg Fuellen
• Keywords: BMCBI 2006, Isoforms, Protein Sequences, SVM Classifier