rMotifGen: Random motif generator for DNA and protein sequences

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Rouchka, Eric C ^a   Timothy, C Timothy ^a  

^a University of Louisville   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; COMMAND LINE INTERFACE; COMPUTATIONAL TOOLS; EVOLUTIONARY MODELS; GRAPHICAL USER INTERFACES (GUI); PLATFORM INDEPENDENCE; POSITION SPECIFIC SCORING MATRIX; USER-DEFINED PARAMETERS;

AMINO ACIDS; BIOINFORMATICS; CHEMICAL DETECTION; DNA; GRAPHICAL USER INTERFACES; MATRIX ALGEBRA; SIGNAL DETECTION;

DNA SEQUENCES;

REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER MODEL; DATA ANALYSIS SOFTWARE; DNA SEQUENCE; GENE INSERTION SEQUENCE; MUTATIONAL ANALYSIS; NUCLEOTIDE BINDING SITE; PROTEIN DOMAIN; PROTEIN MOTIF; QUALITY CONTROL; BIOLOGICAL MODEL; CHEMICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; STATISTICAL MODEL;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BASE SEQUENCE; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 34548385781     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-292     Document Type: Article

References (35)

1. Hu J Li B Kihara D Limitations and potentials of current motif discovery algorithms Nucleic Acids Res 2005 33 4899-4913 1199555 16284194 10.1093/ nar/gki791
2. Lawrence CE Altschul SF Boguski MS Liu JS Neuwald AF Wootton JC Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment Science 1993 262 208-214 10.1126/science.8211139 8211139
3. Neuwald AF Liu JS Lawrence CE Gibbs motif sampling: Detection of bacterial outer membrane protein repeats Protein Sci 1995 4 1618-1632 8520488
4. Thompson W Rouchka EC Lawrence CE Gibbs Recursive Sampler: Finding transcription factor binding sites Nucleic Acids Res 2003 31 3580-3585 169014 12824370 10.1093/nar/gkg608
5. Favorov AV Gelfand MS Gerasimova AV Ravcheev DA Mironov AA Makeev VJ A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length Bioinformatics 2005 21 2240-2245 10.1093/bioinformatics/bti336 15728117
6. Frith MC Hansen U Spouge JL Weng Z Finding functional sequence elements by multiple local alignment Nucleic Acids Res 2004 32 189-200 373279 14704356 10.1093/nar/gkh169
7. Hughes JD Estep PW Tavazoie S Church GM Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae J Mol Biol 2000 296 1205-1214 10.1006/ jmbi.2000.3519 10698627
8. Thijs G Lescot M Marchal K Rombauts S De MB Rouze P Moreau Y A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling Bioinformatics 2001 17 1113-1122 10.1093/bioinformatics/17.12.1113 11751219
9. Workman CT Stormo GD ANN-Spec: A method for discovering transcription factor binding sites with improved specificity Pac Symp Biocomput 2000 467-478 10902194
10. Bailey TL Williams N Misleh C Li WW MEME: Discovering and analyzing DNA and protein sequence motifs Nucleic Acids Res 2006 34 W369-W373 1538909 16845028 10.1093/nar/gkl198
11. Grundy WN Bailey TL Elkan CP Baker ME Meta-MEME: Motif-based hidden Markov models of protein families Comput Appl Biosci 1997 13 397-406 9283754
12. Ao W Gaudet J Kent WJ Muttumu S Mango SE Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR Science 2004 305 1743-1746 10.1126/science.1102216 15375261
13. Hardin CT Rouchka EC DNA Motif Detection Using Particle Swarm Optimization and Expectation-Maximization Proceedings of the 2005 IEEE Swarm Intelligence Symposium 2005
14. Eskin E Pevzner PA Finding composite regulatory patterns in DNA sequences Bioinformatics 2002 18 Suppl 1 S354-S363 12169566
15. Hertz GZ Stormo GD Identifying DNA and protein patterns with statistically significant alignments of multiple sequences Bioinformatics 1999 15 563-577 10.1093/bioinformatics/15.7.563 10487864
16. Liu X Brutlag DL Liu JS BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes Pac Symp Biocomput 2001 127-138 11262934
17. Pavesi G Mereghetti P Mauri G Pesole G Weeder Web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes Nucleic Acids Res 2004 32 W199-W203 441603 15215380 10.1093/nar/gkh465
18. Sinha S Tompa M YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation Nucleic Acids Res 2003 31 3586-3588 169024 12824371 10.1093/nar/gkg618
19. van HJ Rios AF Collado-Vides J Discovering regulatory elements in non-coding sequences by analysis of spaced dyads Nucleic Acids Res 2000 28 1808-1818 102821 10734201 10.1093/nar/28.8.1808
20. Xing EP Wu W Jordan MI Karp RM LOGOS: A modular Bayesian model for de novo motif detection Proc IEEE Comput Soc Bioinform Conf 2003 2 266-276 16452802
21. Pevzner PA Sze SH Combinatorial approaches to finding subtle signals in DNA sequences Proc Int Conf Intell Syst Mol Biol 2000 8 269-278 10977088
22. Tompa M Li N Bailey TL Church GM De MB Eskin E Favorov AV Frith MC Fu Y Kent WJ Makeev VJ Mironov AA Noble WS Pavesi G Pesole G Regnier M Simonis N Sinha S Thijs G van HJ Vandenbogaert M Weng Z Workman C Ye C Zhu Z Assessing computational tools for the discovery of transcription factor binding sites Nat Biotechnol 2005 23 137-144 10.1038/nbt1053 15637633
23. Wingender E Dietze P Karas H Knuppel R TRANSFAC: A database on transcription factors and their DNA binding sites Nucleic Acids Res 1996 24 238-241 145586 8594589 10.1093/nar/24.1.238
24. Engle ML Burks C Artificially generated data sets for testing DNA sequence assembly algorithms Genomics 1993 16 286-288 10.1006/ geno.1993.1180 8486376
25. Coward E Shufflet: Shuffling sequences while conserving the k-let counts Bioinformatics 1999 15 1058-1059 10.1093/bioinformatics/15.12.1058 10745997
26. Rambaut A Grassly NC Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees Comput Appl Biosci 1997 13 235-238 9183526
27. Ponty Y Termier M Denise A GenRGenS: Software for generating random genomic sequences and structures Bioinformatics 2006 22 1534-1535 10.1093/bioinformatics/btl113 16574695
28. Stein L Boulder Data Interchange Format 2002 http://stein.cshl.org/ software/boulder/
29. Bairoch A Boeckmann B The SWISS-PROT protein sequence data bank Nucleic Acids Res 1991 19 Suppl 2247-2249 331359 2041811
30. Schwartz RM Dayhoff M Matrices for detecting distant relationships Atlas of Protein Sequence and Structure Silver Spring, MD, National Biomedical Research Foundation Dayhoff M 1978 353-358
31. Bairoch A UniprotKB/Swiss-Prot Release 52.0 statistics 2007 http://ca.expasy.org/sprot/relnotes/relstat.html 1899100 17202162
32. Matsuda H Taniguchi F Hashimoto A An approach to detection of protein structural motifs using an encoding scheme of backbone conformations Pac Symp Biocomput 1997 280-291 9390299
33. Bairoch A PROSITE: A dictionary of sites and patterns in proteins Nucleic Acids Res 1991 19 Suppl 2241-2245 331358 2041810
34. MEME - Submission form 2006 http://meme.sdsc.edu/meme/meme.html
35. Liu J Gibbs motif sampler 2007 http://www.fas.harvard.edu/~junliu/ Software/gibbs9_95.tar