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  Species-specific analysis of protein sequence motifs using mutual information

Hummel, J., Keshvari, N., Weckwerth, W., & Selbig, J. (2005). Species-specific analysis of protein sequence motifs using mutual information. BMC Bioinformatics, 6, 164. doi:10.1186/1471-2105-6-164.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2BB1-3 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2BB2-1
Genre: Journal Article

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Hummel-2005-Species-specific ana.pdf (Any fulltext), 376KB
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 Creators:
Hummel, J.1, 2, Author              
Keshvari, N.3, Author
Weckwerth, W.4, Author              
Selbig, J.1, Author              
Affiliations:
1BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              
2BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753303              
3External Organizations, ou_persistent22              
4Integrative Proteomics and Metabolomics, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753334              

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Free keywords: mathematical-theory communication
 Abstract: Background: Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions. Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and, in particular, evolutionary features of the underlying sequences. Results: We describe the tool PROfile analysis based on Mutual Information (PROMI) that enables comparative analysis of user-classified protein sequences. PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side. On the client-side platform-independence is achieved by generally applied internet delivery standards. As one possible application analysis of the zinc finger C2H2-type protein domain is introduced to illustrate the functionality of the tool. Conclusion: The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences. It is available at http://promi.mpimpgolm. mpg.de where additional documentation can be found.

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Language(s): eng - English
 Dates: 2005-06-292005
 Publication Status: Published in print
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 Identifiers: ISI: ISI:000230965100001
DOI: 10.1186/1471-2105-6-164
ISSN: 1471-2105 (Electronic) 1471-2105 (Linking)
URI: ://000230965100001 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182352/pdf/1471-2105-6-164.pdf
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Title: BMC Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 6 Sequence Number: - Start / End Page: 164 Identifier: -