Eclair--a web service for unravelling species origin of sequences sampled from mixed host interfaces.
The identification of the genes that participate at the biological interface of two species remains critical to our understanding of the mechanisms of disease resistance, disease susceptibility and symbiosis. The sequencing of complementary DNA (cDNA) libraries prepared from the biological interface between two organisms provides an inexpensive way to identify the novel genes that may be expressed as a cause or consequence of compatible or incompatible interactions. Sequence classification and annotation of species origin typically use an orthology-based approach and require access to large portions of either genome, or a close relative. Novel species- or clade-specific sequences may have no counterpart within existing databases and remain ambiguous features. Here we present a web-service, Eclair, which utilizes support vector machines for the classification of the origin of expressed sequence tags stemming from mixed host cDNA libraries. In addition to providing an interface for the classification of sequences, users are presented with the opportunity to train a model to suit their preferred species pair. Eclair is freely available at http://eclair.btk.fi.
Rudd
Stephen
S
Centre for Biotechnology, Tykistökatu 6 FIN-20521, Turku, Finland. stephen.rudd@btk.utu.fi
Tetko
Igor V
IV
D001185:Artificial Intelligence; D002965:Classification; D019295:Computational Biology / Q000379:methods; D004198:Disease Susceptibility; D020224:Expressed Sequence Tags / Q000737:chemistry*; D015723:Gene Library; D006790:Host-Parasite Interactions; D020407:Internet; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013045:Species Specificity; D013559:Symbiosis; D014584:User-Computer Interface