TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter

Miklos Cserzo; Frank Eisenhaber; Birgit Eisenhaber; Istvan Simon

doi:10.1093/bioinformatics/btg394

TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter

Bioinformatics. 2004 Jan 1;20(1):136-7. doi: 10.1093/bioinformatics/btg394.

Authors

Miklos Cserzo¹, Frank Eisenhaber, Birgit Eisenhaber, Istvan Simon

Affiliation

¹ Agricultural Biotechnology Center, Szent-Gyorgyi A. 4, Gödöllö, H-2100 Hungary.

PMID: 14693825
DOI: 10.1093/bioinformatics/btg394

Abstract

Web-based servers implementing the DAS-TMfilter algorithm have been launched at three mirror sites and their usage is described. The underlying computer program is an upgraded and modified version of the DAS-prediction method. The new server is (approximately 1 among 100 unrelated queries) while the high efficiency of the original algorithm locating TM segments in queries is preserved (sensitivity of approximately 95% among documented proteins with helical TM regions).

Availability: The server operates at three mirror sites: http://mendel.imp.univie.ac.at/sat/DAS/DAS.html, http://wooster.bip.bham.ac.uk/DAS.html and http://www.enzim.hu/DAS/DAS.html. The program is available on request.

Publication types

Evaluation Study
Research Support, Non-U.S. Gov't
Validation Study

MeSH terms

Algorithms*
Amino Acid Sequence
Databases, Protein
False Positive Reactions
Membrane Proteins / chemistry*
Membrane Proteins / classification*
Molecular Sequence Data
Reproducibility of Results
Sensitivity and Specificity
Sequence Alignment / methods*
Sequence Analysis, Protein / methods*
Sequence Homology, Amino Acid*
Software

Substances

Membrane Proteins