Abstract

With the large number of genome sequencing projects completed or underway, a new avenue for finding such candidate regions is rapidly becoming available. Namely, from orthologous sequences collected from a (large) number of species, identify those regions that are best conserved. We have already developed one specialized algorithm that performs such """"""""phylogenetic footprinting"""""""" to identify potential regulatory elements in nucleotide sequences. This algorithm will be both applied to the discovery of novel regulatory elements and extended along multiple axes: 1. Phylogenetic footprinting algorithms will be applied to discover novel regulatory elements in orthologous nucleotide sequences. 2. Phylogenetic footprinting algorithms will be applied to discover novel functional motifs in orthologous protein sequences. 3. Algorithms to discover secondary structure motifs in orthologous RNA molecules will be developed. 4. Algorithms that identify exons from syntenic genomic sequences of multiple species will be developed.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG002602-03
Application #
6786573
Study Section
Genome Study Section (GNM)
Program Officer
Good, Peter J
Project Start
2002-08-07
Project End
2006-07-31
Budget Start
2004-08-01
Budget End
2006-07-31
Support Year
3
Fiscal Year
2004
Total Cost
$326,858
Indirect Cost

  Institution

Name
University of Washington
Department
Biostatistics & Other Math Sci
Type
Schools of Engineering
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195

  Publications

Prakash, Amol; Tompa, Martin (2009) Assessing the discordance of multiple sequence alignments. IEEE/ACM Trans Comput Biol Bioinform 6:542-51
Weinberg, Zasha; Regulski, Elizabeth E; Hammond, Ming C et al. (2008) The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA 14:822-8
Yao, Zizhen; Barrick, Jeffrey; Weinberg, Zasha et al. (2007) A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol 3:e126
Wang, Adrienne X; Ruzzo, Walter L; Tompa, Martin (2007) How accurately is ncRNA aligned within whole-genome multiple alignments? BMC Bioinformatics 8:417
Prakash, Amol; Tompa, Martin (2007) Measuring the accuracy of genome-size multiple alignments. Genome Biol 8:R124
Weinberg, Zasha; Barrick, Jeffrey E; Yao, Zizhen et al. (2007) Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res 35:4809-19
Neph, Shane; Tompa, Martin (2006) MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. Nucleic Acids Res 34:W366-8
Weinberg, Zasha; Ruzzo, Walter L (2006) Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics 22:35-9
Prakash, Amol; Tompa, Martin (2005) Discovery of regulatory elements in vertebrates through comparative genomics. Nat Biotechnol 23:1249-56
Sasson, Ori; Linial, Michal (2005) ProTarget: automatic prediction of protein structure novelty. Nucleic Acids Res 33:W81-4

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