A computational approach for gene assembly and exon annotation based on BLAST

Xutao Deng, Hesham H Ali

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

Abstract

Accurate gene assembly and precise exon annotations are two of the key goals of Human Genome Project. Existing gene reference sequences and exon annotations are far from perfection. This paper introduces a new greedy algorithm which makes use of mRNA reference sequence and BLAST tools from NCBI (National Center for Biotechnology Information) to effectively assemble and annotate gene structures. Four pipelined components are included in this approach. 1. Blast Parser: extract mRNA-DNA local alignment pairs. 2. Chain Finder: transform local alignments to spliced alignment. 3. Assembler: assemble multiple DNA sequences of into a continuous DNA sequence based on their spliced alignments with a given mRNA sequence. 4. Annotator: resolve exon-intron boundary based on splicing signals. Test results on one sample set of human genes show that gene assembly and exon annotation using the proposed approach is significantly better than contig references from NCBI. The software is available upon request.

Original languageEnglish (US)
Title of host publication2005 IEEE International Conference on Electro Information Technology
StatePublished - Dec 1 2005
Event2005 IEEE International Conference on Electro Information Technology - Lincoln, NE, United States
Duration: May 22 2005May 25 2005

Publication series

Name2005 IEEE International Conference on Electro Information Technology
Volume2005

Conference

Conference2005 IEEE International Conference on Electro Information Technology
CountryUnited States
CityLincoln, NE
Period5/22/055/25/05

Fingerprint

Genes
DNA sequences
Biotechnology
DNA
Messenger RNA

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Deng, X., & Ali, H. H. (2005). A computational approach for gene assembly and exon annotation based on BLAST. In 2005 IEEE International Conference on Electro Information Technology [1627022] (2005 IEEE International Conference on Electro Information Technology; Vol. 2005).

A computational approach for gene assembly and exon annotation based on BLAST. / Deng, Xutao; Ali, Hesham H.

2005 IEEE International Conference on Electro Information Technology. 2005. 1627022 (2005 IEEE International Conference on Electro Information Technology; Vol. 2005).

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

Deng, X & Ali, HH 2005, A computational approach for gene assembly and exon annotation based on BLAST. in 2005 IEEE International Conference on Electro Information Technology., 1627022, 2005 IEEE International Conference on Electro Information Technology, vol. 2005, 2005 IEEE International Conference on Electro Information Technology, Lincoln, NE, United States, 5/22/05.
Deng X, Ali HH. A computational approach for gene assembly and exon annotation based on BLAST. In 2005 IEEE International Conference on Electro Information Technology. 2005. 1627022. (2005 IEEE International Conference on Electro Information Technology).
Deng, Xutao ; Ali, Hesham H. / A computational approach for gene assembly and exon annotation based on BLAST. 2005 IEEE International Conference on Electro Information Technology. 2005. (2005 IEEE International Conference on Electro Information Technology).
@inproceedings{30ee16c3e64c49759809840a01ca2ff2,
title = "A computational approach for gene assembly and exon annotation based on BLAST",
abstract = "Accurate gene assembly and precise exon annotations are two of the key goals of Human Genome Project. Existing gene reference sequences and exon annotations are far from perfection. This paper introduces a new greedy algorithm which makes use of mRNA reference sequence and BLAST tools from NCBI (National Center for Biotechnology Information) to effectively assemble and annotate gene structures. Four pipelined components are included in this approach. 1. Blast Parser: extract mRNA-DNA local alignment pairs. 2. Chain Finder: transform local alignments to spliced alignment. 3. Assembler: assemble multiple DNA sequences of into a continuous DNA sequence based on their spliced alignments with a given mRNA sequence. 4. Annotator: resolve exon-intron boundary based on splicing signals. Test results on one sample set of human genes show that gene assembly and exon annotation using the proposed approach is significantly better than contig references from NCBI. The software is available upon request.",
author = "Xutao Deng and Ali, {Hesham H}",
year = "2005",
month = "12",
day = "1",
language = "English (US)",
isbn = "0780392329",
series = "2005 IEEE International Conference on Electro Information Technology",
booktitle = "2005 IEEE International Conference on Electro Information Technology",

}

TY - GEN

T1 - A computational approach for gene assembly and exon annotation based on BLAST

AU - Deng, Xutao

AU - Ali, Hesham H

PY - 2005/12/1

Y1 - 2005/12/1

N2 - Accurate gene assembly and precise exon annotations are two of the key goals of Human Genome Project. Existing gene reference sequences and exon annotations are far from perfection. This paper introduces a new greedy algorithm which makes use of mRNA reference sequence and BLAST tools from NCBI (National Center for Biotechnology Information) to effectively assemble and annotate gene structures. Four pipelined components are included in this approach. 1. Blast Parser: extract mRNA-DNA local alignment pairs. 2. Chain Finder: transform local alignments to spliced alignment. 3. Assembler: assemble multiple DNA sequences of into a continuous DNA sequence based on their spliced alignments with a given mRNA sequence. 4. Annotator: resolve exon-intron boundary based on splicing signals. Test results on one sample set of human genes show that gene assembly and exon annotation using the proposed approach is significantly better than contig references from NCBI. The software is available upon request.

AB - Accurate gene assembly and precise exon annotations are two of the key goals of Human Genome Project. Existing gene reference sequences and exon annotations are far from perfection. This paper introduces a new greedy algorithm which makes use of mRNA reference sequence and BLAST tools from NCBI (National Center for Biotechnology Information) to effectively assemble and annotate gene structures. Four pipelined components are included in this approach. 1. Blast Parser: extract mRNA-DNA local alignment pairs. 2. Chain Finder: transform local alignments to spliced alignment. 3. Assembler: assemble multiple DNA sequences of into a continuous DNA sequence based on their spliced alignments with a given mRNA sequence. 4. Annotator: resolve exon-intron boundary based on splicing signals. Test results on one sample set of human genes show that gene assembly and exon annotation using the proposed approach is significantly better than contig references from NCBI. The software is available upon request.

UR - http://www.scopus.com/inward/record.url?scp=33947142334&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33947142334&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:33947142334

SN - 0780392329

SN - 9780780392328

T3 - 2005 IEEE International Conference on Electro Information Technology

BT - 2005 IEEE International Conference on Electro Information Technology

ER -