A new approach for gene annotation using unambiguous sequence joining

A. Tchourbanov, D. Quest, Hesham H Ali, Mark A Pauley, Robert B Norgren

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Citations (Scopus)

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%.

Original languageEnglish (US)
Title of host publicationProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages353-362
Number of pages10
ISBN (Print)0769520006, 9780769520001
DOIs
StatePublished - 2003
Event2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States
Duration: Aug 11 2003Aug 14 2003

Other

Other2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
CountryUnited States
CityStanford
Period8/11/038/14/03

Fingerprint

Joining
Genes
DNA
DNA sequences
Nucleotides
Messenger RNA

Keywords

  • BLAST
  • dynamic programming
  • RefSeq
  • Spliced alignments

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Science Applications

Cite this

Tchourbanov, A., Quest, D., Ali, H. H., Pauley, M. A., & Norgren, R. B. (2003). A new approach for gene annotation using unambiguous sequence joining. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 (pp. 353-362). [1227336] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSB.2003.1227336

A new approach for gene annotation using unambiguous sequence joining. / Tchourbanov, A.; Quest, D.; Ali, Hesham H; Pauley, Mark A; Norgren, Robert B.

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 353-362 1227336.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Tchourbanov, A, Quest, D, Ali, HH, Pauley, MA & Norgren, RB 2003, A new approach for gene annotation using unambiguous sequence joining. in Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003., 1227336, Institute of Electrical and Electronics Engineers Inc., pp. 353-362, 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, Stanford, United States, 8/11/03. https://doi.org/10.1109/CSB.2003.1227336
Tchourbanov A, Quest D, Ali HH, Pauley MA, Norgren RB. A new approach for gene annotation using unambiguous sequence joining. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc. 2003. p. 353-362. 1227336 https://doi.org/10.1109/CSB.2003.1227336
Tchourbanov, A. ; Quest, D. ; Ali, Hesham H ; Pauley, Mark A ; Norgren, Robert B. / A new approach for gene annotation using unambiguous sequence joining. Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. pp. 353-362
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