skip to main content
10.1145/1854776.1854839acmconferencesArticle/Chapter ViewAbstractPublication PagesbcbConference Proceedingsconference-collections
research-article

An intelligent data-centric approach toward identification of conserved motifs in protein sequences

Published: 02 August 2010 Publication History

Abstract

The continued integration of the computational and biological sciences has revolutionized genomic and proteomic studies. However, efficient collaboration between these fields requires the creation of shared standards. A common problem arises when biological input does not properly fit the expectations of the algorithm, which can result in misinterpretation of the output. This potential confounding of input/output is a drawback especially when regarding motif finding software. Here we propose a method for improving output by selecting input based upon evolutionary distance, domain architecture, and known function. This method improved detection of both known and unknown motifs in two separate case studies. By standardizing input considerations, both biologists and bioinformaticians can better interpret and design the evolving sophistication of bioinformatic software.

References

[1]
Hedges SB, J Blair, M Venturi, J Shoe. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evolutionary Biology. 2004; 4:2.
[2]
Kumar S, Filipski A, Swarna V, Walker A, Hedges SB. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proceedings of the Natural Academy of Sciences. 27 Dec 2005; 102(52):18842--18847.
[3]
Quest D, K Dempsey, M Shafiullah, D Bastola, and H Ali. MTAP: A Motif Tool Assessment Pipeline for Automated Assessment of De Novo Regulatory Motif Discovery Tool. BMC Bioinformatics. 2008 Aug 12; 9 Suppl 9:S6.
[4]
Tompa M, N Li, T Bailey, G Church, B DeMoor, E Eskin, A Favorov, M Frith, Y Fu, W Kent, V Makeev, A Mironov, W Noble, G Pavesi, G Pesole, M Regnier, N Simonis, S Sinha, G Thijs, J. van Helden, M Vandenbogaert, Z Weng, C Workman, C Ye, and Z Zhu. Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites. Z Nature Biotechnology. 1 Jan 2005; 23(1):137--144.
[5]
Zheng, J., et al., Prestin is the motor protein of cochlear outer hair cells. Nature, 2000. 405(6783): p. 149--55.
[6]
Dorwart, M. R., et al., The solute carrier 26 family of proteins in epithelial ion transport. Physiology (Bethesda), 2008. 23: p. 104--14.
[7]
Yarov-Yarovoy V, Baker D, Catterall WA. Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proc Natl Acad Sci USA, 2006 May 9; 103(19):7292--7. Epub 2006 Apr 28.
[8]
Haitin Y, Yisharel I, Malka E, Shamgar L, Schottelndreier H, Peretz A, Paas Y, Attali B. S1 constraints in the voltage sensor domain of Kv7.1 K+ channels. PLoS One. 2008 Apr 9; 3(4):e1935.
[9]
Heginbotham K, Lu Z, Abramson T, MacKinnon R. Mutations in the K+ channel signature sequence. Biophys J. 1994 Apr; 66(4):1061--7.
[10]
Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Res, 14:1188--1190, (2004)

Cited By

View all
  • (2015)Applications of High Performance Computing in Bioinformatics, Computational Biology and Computational ChemistryBioinformatics and Biomedical Engineering10.1007/978-3-319-16480-9_51(527-541)Online publication date: 2015
  • (2013)A New Approach for Sequence AnalysisBioinformatics10.4018/978-1-4666-3604-0.ch079(1536-1556)Online publication date: 2013
  • (2012)HPCS 2012 tutorials: Tutorial I: High performance computing in biomedical informatics2012 International Conference on High Performance Computing & Simulation (HPCS)10.1109/HPCSim.2012.6266878(1-17)Online publication date: Jul-2012
  • Show More Cited By
  1. An intelligent data-centric approach toward identification of conserved motifs in protein sequences

    Recommendations

    Comments

    Information & Contributors

    Information

    Published In

    cover image ACM Conferences
    BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
    August 2010
    705 pages
    ISBN:9781450304382
    DOI:10.1145/1854776
    Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

    Sponsors

    Publisher

    Association for Computing Machinery

    New York, NY, United States

    Publication History

    Published: 02 August 2010

    Permissions

    Request permissions for this article.

    Check for updates

    Author Tags

    1. intelligent tools
    2. motif finding
    3. prestin
    4. protein sequences

    Qualifiers

    • Research-article

    Conference

    BCB'10
    Sponsor:

    Acceptance Rates

    Overall Acceptance Rate 254 of 885 submissions, 29%

    Contributors

    Other Metrics

    Bibliometrics & Citations

    Bibliometrics

    Article Metrics

    • Downloads (Last 12 months)1
    • Downloads (Last 6 weeks)0
    Reflects downloads up to 17 Jan 2025

    Other Metrics

    Citations

    Cited By

    View all
    • (2015)Applications of High Performance Computing in Bioinformatics, Computational Biology and Computational ChemistryBioinformatics and Biomedical Engineering10.1007/978-3-319-16480-9_51(527-541)Online publication date: 2015
    • (2013)A New Approach for Sequence AnalysisBioinformatics10.4018/978-1-4666-3604-0.ch079(1536-1556)Online publication date: 2013
    • (2012)HPCS 2012 tutorials: Tutorial I: High performance computing in biomedical informatics2012 International Conference on High Performance Computing & Simulation (HPCS)10.1109/HPCSim.2012.6266878(1-17)Online publication date: Jul-2012
    • (2011)A New Approach for Sequence AnalysisHandbook of Research on Computational and Systems Biology10.4018/978-1-60960-491-2.ch009(202-223)Online publication date: 2011

    View Options

    Login options

    View options

    PDF

    View or Download as a PDF file.

    PDF

    eReader

    View online with eReader.

    eReader

    Media

    Figures

    Other

    Tables

    Share

    Share

    Share this Publication link

    Share on social media