Methodology article
SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics
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* Corresponding author: Fabrice Touzain touzain@loria.fr
1 Laboratoire Lorrain de Recherche en Informatique et ses Applications, Campus Scientifique, B.P. 239, UMR CNRS-INPL-INRIA-Nancy 2-UHP 7503, 54506 Vandœuvre-lès-Nancy, France
2 Unité Mathématique, Informatique et Génome, INRA, 78350 Jouy-en-Josas, France
3 Laboratoire de Génétique et Microbiologie, UMR INRA 1128, IFR 110, Université Henri Poincaré, B.P. 239, 54506 Vandœuvre-lès-Nancy, France
4 Laboratoire d'Informatique Fondamentale de Lille, UMR USTL-CNRS 8022, 59655 Villeneuve d'Ascq, France
BMC Bioinformatics 2008, 9:73 doi:10.1186/1471-2105-9-73
Published: 31 January 2008Additional files
Additional file 1:
Summary of results for Streptomyces. Summary of results. Interesting motifs given by SIGffRid when applied on S. coelicolor and S. avermitilis and comparison with known σ factor binding sites. Are given motifs whose occurrences overlap known SFBS (known motif is given in front of the name of the concerned Sigma factor).
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Additional file 2:
SIGffRid motifs related to SigR. SIGffRid predictions related to the SigR target sequence in S. coelicolor. Gene functions and putative binding sites for SigR σ factor or its homologue(s). It shows overlaps of binding sites of the various motif declinations for SigR binding site.
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Additional file 3:
SIGffRid motifs related to BldN. BldN related motif. Gene functions and putative binding sites for BldN σ factor in S. coelicolor.
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Additional file 4:
SIGffRid motifs possibly related to recA promoter motif. Interesting motif related to recA promoter motif. Gene functions and putative regulatory binding sites for DNA-damage related motifs (recA promoter) in S. coelicolor.
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Additional file 5:
SIGffRid motifs similar to known E. coli, S. typhimurium, B. subtilis, or B. licheniformis SFBSs. SIGffRid results compared with known SFBS motifs in E. coli/S. typhymurium on one hand, and B. subtilis/B. licheniformis on the other hand. Interesting results obtained from E. coli K12/S. typhimurium LT2 and B. subtilis 168/B. licheniformis ATCC 14580 pairs of bacterial genomes by using all pairs of orthologues.
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