AGenDA: homology-based gene prediction.
We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.
Taher
Leila
L
International Graduate School for Bioinformatics and Genome Research University of Bielefeld, Postfach 10 01 31, 33501 Bielefeld, Germany. ltaher@TechFak.Uni-Bielefeld.DE
Rinner
Oliver
O
Garg
Saurabh
S
Sczyrba
Alexander
A
Brudno
Michael
M
Batzoglou
Serafim
S
Morgenstern
Burkhard
B
D000465:Algorithms; D034742:Electronic Mail; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software