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Reliability of transmembrane predictions in whole-genome data
Ctr. for Genomics and Bioinformatics, Karolinska Institutet.ORCID iD: 0000-0001-5689-9797
2002 (English)In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 532, no 3, 415-418 p.Article in journal (Refereed) Published
Abstract [en]

Transmembrane prediction methods are generally benchmarked on a set of proteins with experimentally verified topology. We have investigated if the accuracy measured on such datasets can be expected in an unbiased genomic analysis, or if there is a bias towards 'easily predictable' proteins in the benchmark datasets. As a measurement of accuracy, the concordance of the results from five different prediction methods was used (TMHMM, PHD, HMMTOP, MEMSAT, and TOPPRED). The benchmark dataset showed significantly higher levels (up to five times) of agreement between different methods than in 10 tested genomes. We have also analyzed which programs are most prone to make mispredictions by measuring the frequency of one-out-of-five disagreeing predictions.

Place, publisher, year, edition, pages
2002. Vol. 532, no 3, 415-418 p.
Keyword [en]
Membrane protein, Prediction, Reliability, Topology
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-48867DOI: 10.1016/S0014-5793(02)03730-4ISI: 000179884800028PubMedID: 12482603OAI: oai:DiVA.org:kth-48867DiVA: diva2:458721
Note
QC 20111124Available from: 2011-11-23 Created: 2011-11-23 Last updated: 2017-12-08Bibliographically approved

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Käll, Lukas

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