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A combined transmem...
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Käll, LukasCtr. for Genomics and Bioinformatics, Karolinska Institutet
(författare)
A combined transmembrane topology and signal peptide prediction method
- Artikel/kapitelEngelska2004
Förlag, utgivningsår, omfång ...
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Elsevier BV,2004
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printrdacarrier
Nummerbeteckningar
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LIBRIS-ID:oai:DiVA.org:kth-48866
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https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-48866URI
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https://doi.org/10.1016/j.jmb.2004.03.016DOI
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http://kipublications.ki.se/Default.aspx?queryparsed=id:1932473URI
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Språk:engelska
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Sammanfattning på:engelska
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Ämneskategori:ref swepub-contenttype
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Ämneskategori:art swepub-publicationtype
Anmärkningar
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QC 20111124
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An inherent problem in transmembrane protein topology prediction and signal peptide prediction is the high similarity between the hydrophobic regions of a transmembrane helix and that of a signal peptide, leading to cross-reaction between the two types of predictions. To improve predictions further, it is therefore important to make a predictor that aims to discriminate between the two classes. In addition, topology information can be gained when successfully predicting a signal Peptide leading a trans' membrane protein since it dictates that the N terminus of the mature protein must be on the non-cytoplasmic side of the membrane. Here, we present Phobius, a combined transmembrane protein topology and signal peptide predictor. The predictor is based on a hidden Markov model (HMM) that models the different sequence regions of a signal peptide and the different regions of a transmembrane protein in a series of interconnected states. Training was done on a newly assembled and curated dataset. Compared to TMHMM and SignalP, errors coming from cross-prediction between transmembrane segments and signal peptides were reduced substantially by Phobius. False classifications of signal peptides were reduced from 26.1% to 3.9% and false classifications of transmembrane helices were reduced from 19.0%, to 7.7%. Phobius was applied to the proteomes of Honzo sapiens and Escherichia coli. Here we also noted a drastic reduction of false classifications compared to TMHMM/SignalP, suggesting that Phobius is well suited for whole-genome annotation of signal peptides and transmembrane regions. The method is available at http://phobius.cgb.ki.se/ as well as at http://phobius.binf.ku.dk/.
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Biuppslag (personer, institutioner, konferenser, titlar ...)
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Krogh, Anders
(författare)
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Sonnhammer, Erik L. L.
(författare)
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Ctr. for Genomics and Bioinformatics, Karolinska Institutet
(creator_code:org_t)
Sammanhörande titlar
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Ingår i:Journal of Molecular Biology: Elsevier BV338:5, s. 1027-10360022-28361089-8638
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