GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.
GeneAlign is a coding exon prediction tool for predicting protein coding genes by measuring the homologies between a sequence of a genome and related sequences, which have been annotated, of other genomes. Identifying protein coding genes is one of most important tasks in newly sequenced genomes. With increasing numbers of gene annotations verified by experiments, it is feasible to identify genes in the newly sequenced genomes by comparing to annotated genes of phylogenetically close organisms. GeneAlign applies CORAL, a heuristic linear time alignment tool, to determine if regions flanked by the candidate signals (initiation codon-GT, AG-GT and AG-STOP codon) are similar to annotated coding exons. Employing the conservation of gene structures and sequence homologies between protein coding regions increases the prediction accuracy. GeneAlign was tested on Projector dataset of 491 human-mouse homologous sequence pairs. At the gene level, both the average sensitivity and the average specificity of GeneAlign are 81%, and they are larger than 96% at the exon level. The rates of missing exons and wrong exons are smaller than 1%. GeneAlign is a free tool available at http://genealign.hccvs.hc.edu.tw.
Hsieh
Shu Ju
SJ
Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, 300, ROC.
Lin
Chun Yuan
CY
Liu
Ning Han
NH
Chow
Wei Yuan
WY
Tang
Chuan Yi
CY
D000818:Animals; D005091:Exons; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D051379:Mice; D010802:Phylogeny; D011506:Proteins / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface
D011506:Proteins