Heider, Dominik; Verheyen, Jens; Hoffmann, Daniel:
Machine learning on normalized protein sequences
In: BMC Research Notes, Band 4 (2011), S. 94
2011Artikel/Aufsatz in ZeitschriftOA Gold
InformatikBiologieMedizinFakultät für Biologie » Bioinformatics and Computational BiophysicsForschungszentren » Zentrum für Medizinische Biotechnologie (ZMB)
Damit verbunden: 1 Publikation(en)
Titel in Englisch:
Machine learning on normalized protein sequences
Autor*in:
Heider, DominikUDE
LSF ID
50610
Sonstiges
der Hochschule zugeordnete*r Autor*in
;
Verheyen, Jens;Hoffmann, DanielUDE
GND
1214304125
LSF ID
16263
ORCID
0000-0003-2973-7869ORCID iD
Sonstiges
der Hochschule zugeordnete*r Autor*in
Erscheinungsjahr:
2011
Open Access?:
OA Gold
DuEPublico 1 ID
Notiz:
OA Förderung 2011
Sprache des Textes:
Englisch

Abstract in Englisch:

Background Machine learning techniques have been widely applied to biological sequences, e.g. to predict drug resistance in HIV-1 from sequences of drug target proteins and protein functional classes. As deletions and insertions are frequent in biological sequences, a major limitation of current methods is the inability to handle varying sequence lengths. Findings We propose to normalize sequences to uniform length. To this end, we tested one linear and four different non-linear interpolation methods for the normalization of sequence lengths of 19 classification datasets. Classification tasks included prediction of HIV-1 drug resistance from drug target sequences and sequence-based prediction of protein function. We applied random forests to the classification of sequences into "positive" and "negative" samples. Statistical tests showed that the linear interpolation outperforms the non-linear interpolation methods in most of the analyzed datasets, while in a few cases non-linear methods had a small but significant advantage. Compared to other published methods, our prediction scheme leads to an improvement in prediction accuracy by up to 14%. Conclusions We found that machine learning on sequences normalized by simple linear interpolation gave better or at least competitive results compared to state-of-the-art procedures, and thus, is a promising alternative to existing methods, especially for protein sequences of variable length.