Universal seeds for cDNA-to-genome comparison.

BMC Bioinformatics
Leming ZhouLiliana Florea

Abstract

To meet the needs of gene annotation for newly sequenced organisms, optimized spaced seeds can be implemented into cross-species sequence alignment programs to accurately align gene sequences to the genome of a related species. So far, seed performance has been tested for comparisons between closely related species, such as human and mouse, or on simulated data. As the number and variety of genomes increases, it becomes desirable to identify a small set of universal seeds that perform optimally or near-optimally on a large range of comparisons. Using statistical regression methods, we investigate the sensitivity of seeds, in particular good seeds, between four cDNA-to-genome comparisons at different evolutionary distances (human-dog, human-mouse, human-chicken and human-zebrafish), and identify classes of comparisons that show similar seed behavior and therefore can employ the same seed. In addition, we find that with high confidence good seeds for more distant comparisons perform well on closer comparisons, within 98-99% of the optimal seeds, and thus represent universal good seeds. We show for the first time that optimal and near-optimal seeds for distant species-to-species comparisons are more generally applicable to a wide ...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Apr 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·W R Pearson, D J Lipman
Jun 15, 1996·Genomics·M Burset, R Guigó
Apr 25, 1997·Journal of Molecular Biology·C Burge, S Karlin
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 1, 1997·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Z ZhangW Miller
Apr 6, 2002·Bioinformatics·Bin MaMing Li
Jan 17, 2003·Genome Research·Scott SchwartzWebb Miller
Dec 19, 2003·Nucleic Acids Research·David L WheelerLukas Wagner
Feb 7, 2004·Bioinformatics·Kwok Pui ChoiLouxin Zhang
Aug 4, 2004·Journal of Bioinformatics and Computational Biology·Broña BrejováTomás Vinar
Oct 16, 2004·BMC Bioinformatics·Laurent Noé, Gregory Kucherov
Jan 6, 2005·Genome Research·Liliana FloreaGranger Sutton
Aug 20, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yanni Sun, Jeremy Buhler
Nov 25, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Franco P PreparataKwok Pui Choi
Dec 31, 2005·Nucleic Acids Research·Cathy H WuBaris Suzek
Jul 5, 2006·Journal of Bioinformatics and Computational Biology·Gregory KucherovMikhail Roytberg
Dec 16, 2006·Nucleic Acids Research·David L WheelerEugene Yaschenko
Apr 26, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Leming Zhou, Liliana Florea
Nov 30, 2007·Nucleic Acids Research·David L WheelerEugene Yaschenko

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Citations

May 12, 2009·Nucleic Acids Research·Leming ZhouLiliana Florea
Oct 12, 2010·Advances in Bioinformatics·Laurent NoéGregory Kucherov
Mar 5, 2010·BMC Bioinformatics·Won-Hyoung Chung, Seong-Bae Park
Feb 5, 2014·Nucleic Acids Research·Martin C Frith, Laurent Noé
Aug 1, 2009·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Mikhail RoytbergGregory Kucherov
Oct 23, 2008·Bioinformatics·Leming ZhouLiliana Florea

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Software Mentioned

UCSC Genome Browser
ESTmapper
Sim4
blast
R
Fastx
blastz
PatternHunter

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