TY  - JOUR
AB  - Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprinting: they exploit the fact that functionally important regions in genomic sequences are usually more conserved than non-functional regions. We created a WWW-based software program for homology-based gene prediction at BiBiServ (Bielefeld Bioinformatics Server). Our tool takes pairs of evolutionary related genomic sequences as input data, e.g. from human and mouse. The server runs CHAOS and DIALIGN to create an alignment of the input sequences and subsequently searches for conserved splicing signals and start/stop codons near regions of local sequence conservation. Genes are predicted based on local homology information and splice signals. The server returns predicted genes together with a graphical representation of the underlying alignment. The program is available at http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/.
DA  - 2004
DO  - 10.1093/nar/gkh386
KW  - *Genomics
KW  - DNA
KW  - Sequence Homology
KW  - Sequence Analysis
KW  - RNA Splicing
KW  - Sequence Alignment
KW  - Phylogeny
KW  - Nucleic Acid
KW  - Humans
KW  - *Genes
KW  - Conserved Sequence
KW  - DNA Footprinting
KW  - Animals
KW  - Base Sequence
KW  - Internet
KW  - Mice
KW  - *Software
LA  - eng
IS  - Web Server
M2  - W305
PY  - 2004
SN  - 0305-1048
SP  - W305-W308
T2  - Nucleic Acids Research
TI  - AGenDA: gene prediction by cross-species sequence comparison
UR  - https://nbn-resolving.org/urn:nbn:de:0070-pub-16074005
Y2  - 2024-11-21T22:17:53
ER  -