A New Approach for Gene Annotation Using Unambiguous Sequence Joining

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IEEE Computer Society Bioinformatics Conference (CSB'03)

Stanford, California

August 11-August 14

ISBN: 0-7695-2000-6

	ASCII Text	x
	Alexandre Tchourbanov, Daniel Quest, Hesham Ali, Mark Pauley, Robert Norgren, "A New Approach for Gene Annotation Using Unambiguous Sequence Joining," Computational Systems Bioinformatics Conference, International IEEE Computer Society, pp. 353, IEEE Computer Society Bioinformatics Conference (CSB'03), 2003.

	BibTex	x
	@article{ 10.1109/CSB.2003.1227336, author = {Alexandre Tchourbanov and Daniel Quest and Hesham Ali and Mark Pauley and Robert Norgren}, title = {A New Approach for Gene Annotation Using Unambiguous Sequence Joining}, journal ={Computational Systems Bioinformatics Conference, International IEEE Computer Society}, volume = {0}, year = {2003}, isbn = {0-7695-2000-6}, pages = {353}, doi = {http://doi.ieeecomputersociety.org/10.1109/CSB.2003.1227336}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - CONF JO - Computational Systems Bioinformatics Conference, International IEEE Computer Society TI - A New Approach for Gene Annotation Using Unambiguous Sequence Joining SN - 0-7695-2000-6 SP EP A1 - Alexandre Tchourbanov, A1 - Daniel Quest, A1 - Hesham Ali, A1 - Mark Pauley, A1 - Robert Norgren, PY - 2003 KW - Spliced alignments KW - BLAST KW - RefSeq KW - dynamic programming VL - 0 JA - Computational Systems Bioinformatics Conference, International IEEE Computer Society ER -

Alexandre Tchourbanov, University of Nebraska

Daniel Quest, University of Nebraska

Hesham Ali, University of Nebraska

Mark Pauley, University of Nebraska

Robert Norgren, University of Nebraska

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/CSB.2003.1227336

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 non-canonic 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%.

Index Terms:

Spliced alignments, BLAST, RefSeq, dynamic programming

Citation:

Alexandre Tchourbanov, Daniel Quest, Hesham Ali, Mark Pauley, Robert Norgren, "A New Approach for Gene Annotation Using Unambiguous Sequence Joining," csb, pp.353, IEEE Computer Society Bioinformatics Conference (CSB'03), 2003

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