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

Xutao Deng; Hesham H. Ali

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

Xutao Deng, Hesham H. Ali

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English (US)
Title of host publication	2005 IEEE International Conference on Electro Information Technology
State	Published - 2005
Event	2005 IEEE International Conference on Electro Information Technology - Lincoln, NE, United States Duration: May 22 2005 → May 25 2005

Publication series

Name	2005 IEEE International Conference on Electro Information Technology
Volume	2005

Conference

Conference	2005 IEEE International Conference on Electro Information Technology
Country/Territory	United States
City	Lincoln, NE
Period	5/22/05 → 5/25/05

ASJC Scopus subject areas

General Engineering

Cite this

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.

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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",

language = "English (US)",

isbn = "0780392329",

series = "2005 IEEE International Conference on Electro Information Technology",

booktitle = "2005 IEEE International Conference on Electro Information Technology",

note = "2005 IEEE International Conference on Electro Information Technology ; Conference date: 22-05-2005 Through 25-05-2005",

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AU - Deng, Xutao

AU - Ali, Hesham H.

PY - 2005

Y1 - 2005

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.

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M3 - Conference contribution

AN - SCOPUS:33947142334

SN - 0780392329

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T3 - 2005 IEEE International Conference on Electro Information Technology

BT - 2005 IEEE International Conference on Electro Information Technology

T2 - 2005 IEEE International Conference on Electro Information Technology

Y2 - 22 May 2005 through 25 May 2005

ER -

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

Abstract

Publication series

Conference

ASJC Scopus subject areas

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