A new approach for gene annotation using unambiguous sequence joining

Author

Tchourbanov, Alexandre ; Quest, Daniel ; Ali, Hesham ; Pauley, Mark ; Norgren, R.

Author_Institution

Dept. of Comput. Sci., Nebraska Univ., Omaha, NE, USA

fYear

2003

fDate

11-14 Aug. 2003

Firstpage

353

Lastpage

362

Abstract

The problem addressed by this paper is accurate and automatic gene annotation following precise identification/annotation of exon and intron boundaries of biologically verified nucleotide sequences using the alignment of human genomic DNA to curated mRNA transcripts. We provide a detailed description of a new cDNA/DNA homology gene annotation algorithm that combines the results of BLASTN searches and spliced alignments. Compared to other programs currently in use, annotation quality is significantly increased through the unambiguous junction of genomic DNA sequences. We also address gene annotation with both noncanonic splice sites and short exons. The approach has been tested on the genie learning subset as well as full-scale human RefSeq, and has demonstrated performance as high as 97%.

Keywords

DNA; biology computing; dynamic programming; genetic algorithms; genetics; molecular biophysics; sequential decoding; BLASTN searches; dynamic programming; exon; full-scale human RefSeq; gene annotation; genie learning subset; human genomic DNA; intron; mRNA transcripts; noncanonic splice sites; nucleotide sequences; sequence joining; spliced alignments; Bioinformatics; Computer science; DNA; Databases; Educational institutions; Genomics; Humans; Proteins; Sequences; Testing;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE

Print_ISBN

0-7695-2000-6

Type

conf

DOI

10.1109/CSB.2003.1227336

Filename

1227336