rMotifGen: random motif generator for DNA and protein sequences.

rMotifGen: random motif generator for DNA and protein sequences. Research Abstract Details 

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rMotifGen: random motif generator for DNA and protein sequences. Abstract Text:

Eric C Rouchka,C Timothy Hardin,

BACKGROUND: Detection of short, subtle conserved motif regions within a set of related DNA or amino acid sequences can lead to discoveries about important regulatory domains such as transcription factor and DNA binding sites as well as conserved protein domains. In order to help assess motif detection algorithms on motifs with varying properties and levels of conservation, we have developed a computational tool, rMotifGen, with the sole purpose of generating a number of random DNA or protein sequences containing short sequence motifs. Each motif consensus can be user-defined, randomly generated, or created from a position-specific scoring matrix (PSSM). Insertions and mutations within these motifs are created according to user-defined parameters and substitution matrices. The resulting sequences can be helpful in mutational simulations and in testing the limits of motif detection algorithms. RESULTS: Two implementations of rMotifGen have been created, one providing a graphical user interface (GUI) for random motif construction, and the other serving as a command line interface. The second implementation has the added advantages of platform independence and being able to be called in a batch mode. rMotifGen was used to construct sample sets of sequences containing DNA motifs and amino acid motifs that were then tested against the Gibbs sampler and MEME packages. CONCLUSION: rMotifGen provides an efficient and convenient method for creating random DNA or amino acid sequences with a variable number of motifs, where the instance of each motif can be incorporated using a position-specific scoring matrix (PSSM) or by creating an instance mutated from its corresponding consensus using an evolutionary model based on substitution matrices. rMotifGen is freely available at: http://bioinformatics.louisville.edu/brg/rMotifGen/.

rMotifGen: random motif generator for DNA and protein sequences. Publishing Authors By Initials

EC Rouchka,CT Hardin,

For similar information science: computing methodologies: software research abstracts see: information science: computing methodologies: software research

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rMotifGen: random motif generator for DNA and protein sequences. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: BMC bioinformatics

VOLUME: 8

Page Numbers: 292

Journal Abbreviation: BMC Bioinformatics

ISSN: 1471-2105

DAY: 7

MONTH: 08

YEAR: 2007

rMotifGen: random motif generator for DNA and protein sequences. Information

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LANGUAGE: eng

NlmUniqueID: 100965194

rMotifGen: random motif generator for DNA and protein sequences. Keywords Mesh Terms:

KEYWORDS: Software

MESH TERMS: methods

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Grant and Affiliation Information for rMotifGen: random motif generator for DNA and protein sequences.

AFFILIATION: Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA. eric.rouchka@louisville.edu

Country: England

AGENCY: United States NCRR

GRANT: P20RR-16481

ACRONYM: RR

MEDLINETA: BMC Bioinformatics

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