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A New Approach for Gene Annotation Using Unambiguous Sequence Joining
Stanford, California August 11-August 14
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/CSB.2003.1227336IEEE Computer Society Bioinformatics ...
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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
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@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
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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
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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