title: AUGUSTUS: ab initio prediction of alternative transcripts.
abstract: AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing. Herein, we present a WWW server for an extended version of AUGUSTUS that is able to predict multiple splice variants. To our knowledge, this is the first ab initio gene finder that can predict multiple transcripts. In addition, we offer a motif searching facility, where user-defined regular expressions can be searched against putative proteins encoded by the predicted genes. The AUGUSTUS web interface and the downloadable open-source stand-alone program are freely available from http://augustus.gobics.de.
authors.affiliation: Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Göttingen, Germany. mstanke@gwdg.de
authors.forename: Mario
authors.initials: M
authors.lastname: Stanke
authors.forename: Oliver
authors.initials: O
authors.lastname: Keller
authors.forename: Irfan
authors.initials: I
authors.lastname: Gunduz
authors.forename: Alec
authors.initials: A
authors.lastname: Hayes
authors.forename: Stephan
authors.initials: S
authors.lastname: Waack
authors.forename: Burkhard
authors.initials: B
authors.lastname: Morgenstern
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D005091:Exons; D015870:Gene Expression; D005796:Genes; D006801:Humans; D020407:Internet; D007438:Introns; D008390:Markov Chains; D011506:Proteins / Q000235:genetics* / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins