Bacterial syntenies: An exact approach with gene quorum

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Deniélou, Yves Pol ^a   Sagot, Marie France ^a,b   Boyer, Frédéric ^b   Viari, Alain ^a  

^a INRIA RHÔNE ALPES   (France)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC IDENTIFICATION; BACTERIAL SPECIES; COMPARATIVE GENOMICS; FLEXIBLE DEFINITION; FUNCTIONAL GENES; MULTIPLE ALIGNMENT; MULTIPLE SPECIES; VERSATILE TOOLS;

AUTOMATION; BACTERIA; CONSERVATION; TOOLS;

GENES;

BACTERIA (MICROORGANISMS);

ALGORITHM; ARTICLE; BACTERIAL GENOME; BACTERIUM; GENE EXPRESSION REGULATION; GENE ORDER; GENETICS; SYNTENY;

ALGORITHMS; BACTERIA; GENE EXPRESSION REGULATION, BACTERIAL; GENE ORDER; GENOME, BACTERIAL; SYNTENY;

EID: 79956221364     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-193     Document Type: Article

References (37)

1. NCBI: Complete Microbial Genomes. , http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
2. Huynen M, Bork P. Measuring genome evolution. Proc Natl Acad Sci USA 1998, 95:5849-5856. 10.1073/pnas.95.11.5849, 34486, 9600883.
3. Koonin E, Wolf Y. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucl Acids Res 2008, 36:6688-6719. 10.1093/nar/gkn668, 2588523, 18948295.
4. Itoh T, Takemoto K, Mori H, Gojobori T. Evolutionary Instability of Operon Structures Disclosed by Sequence Comparisons of Complete Microbial Genomes. Mol Biol Evol 1999, 16:332-346.
5. Dandekar T, Snel B, Huynen M, P B. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem Sci 1998, 23:324-328. 10.1016/S0968-0004(98)01274-2, 9787636.
6. Tesler G. GRIMM: genome rearrangements web server. Bioinformatics 2002, 18(3):492-493. 10.1093/bioinformatics/18.3.492, 11934753.
7. Sinha A, Meller J. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics 2007, 8:82. 10.1186/1471-2105-8-82, 1821339, 17343765.
8. Uno T, Yagiura M. Fast Algorithms to Enumerate All Common Intervals of Two Permutations. Algorithmica 2000, 26.
9. Heber S, Stoye J. Algorithms for Finding Gene Clusters. WABI: International Workshop on Algorithms in Bioinformatics, LNCS 2001,
10. Didier G. Common intervals of two sequences. Algorithms in Bioinformatics Proceedings, Volume 2812 of Lecture Notes in Bioinformatics 2003, 17-24.
11. Bergeron A, Corteel S, Raffinot M. The Algorithmic of Gene Teams. WABI: International Workshop on Algorithms in Bioinformatics, Volume 2452 of Lecture Notes in Computer Science 2002, 464-476.
12. He X, Goldwasser M. Identifying Conserved Gene Clusters in the Presence of Homology Families. J Comput Biol 2005, 12(6):638-656. 10.1089/cmb.2005.12.638, 16108708.
13. Pasek S, Bergeron A, Risler J, Louis A, Ollivier E, Raffinot M. Identification of genomic features using microsyntenies of domains: Domain teams. Genome Res 2005, 15(6):867-874. 10.1101/gr.3638405, 1142477, 15899966.
14. Kim S, Choi JH, Yang J. Gene Teams with Relaxed Proximity Constraint. IEEE Computational Systems Bioinformatics Conference (CSB 2005) 2005, 44-55.
15. Ling X, He X, Xin D, Han J. Efficiently Identifying Max-Gap Clusters in Pairwise Genome Comparison. J Comput Biol 2008, 15(6):593-609. 10.1089/cmb.2008.0010, 18631023.
16. Ling X, He X, Xin D. Detecting gene clusters under evolutionary constraint in a large number of genomes. Bioinformatics 2009, 25(5):571-577. 10.1093/bioinformatics/btp027, 19158161.
17. Boyer F, Morgat A, Labarre L, Pothier J, Viari A. Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data. Bioinformatics 2005, 21(23):4209-4215. 10.1093/bioinformatics/bti711, 16216829.
18. Calabrese P, Chakravarty S, Vision T. Fast identification and statistical evaluation of segmental homologies in comparative maps. ISMB (Supplement of Bioinformatics), Volume 19 2003, 74-80.
19. Haas B, Delcher A, Wortman J, Salzberg S. DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 2004, 20(18):3643-3646. 10.1093/bioinformatics/bth397, 15247098.
20. Wang X, Shi X, Li Z, Zhu Q, Kong L, Tang W, Ge S, Luo J. Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics 2006, 7:447. 10.1186/1471-2105-7-447, 1626491, 17038171.
21. Rödelsperger C, Dieterich C. Syntenator: multiple gene order alignments with a gene-specific scoring function. Algorithms for Molecular Biology 2008, 3:14. 10.1186/1748-7188-3-14, 2590594, 18990215.
22. Rödelsperger C, Dieterich C. CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes. PloS one 2010, 5:e8861. 10.1371/journal.pone.0008861, 2812507, 20126624.
23. Denielou YP, Boyer F, Viari A, Sagot MF. Multiple Alignment of Biological Networks: A Flexible Approach. CPM: 20th Symposium on Combinatorial Pattern Matching, Volume 5577 of Lecture Notes in Computer Science 2009, 263-273.
24. Ogata H, Fujibuchi W, Goto S, Kanehisa M. A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucl Acids Res 2000, 28(20):4021-4028. 10.1093/nar/28.20.4021, 110779, 11024183.
25. Kalaev M, Bafna V, Sharan R. Fast and Accurate Alignment of Multiple Protein Networks. International Conference on Research in Computational Molecular Biology RECOMB 2008, Volume 4955 of Lecture Notes in Computer Science 2008, 246-256.
26. Simillion C, Vandepoele K, Saeys Y, Van de Peer Y. Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res 2004, 14(6):1095-1106. 10.1101/gr.2179004, 419788, 15173115.
27. Remm M, Storm C, Sonnhammer E. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 2001, 314:1041-1052. 10.1006/jmbi.2000.5197, 11743721.
28. Altenhoff A, Dessimoz C. Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PloS Comput Biol 2009, 5:e1000262+. 2612752, 19148271.
29. Habib M, Paul C, Raffinot M. Maximal Common Connected Sets of Interval Graphs. CPM: 15th Symposium on Combinatorial Pattern Matching, Volume 3109 of Lecture Notes in Computer Science 2004, 347-358.
30. Vandepoele K, Saeys Y, Simillion C, Raes J, Van De Peer Y. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res 2002, 12(11):1792-1801. 10.1101/gr.400202, 187543, 12421767.
31. Simillion C, Janssens K, Sterck L, Van de Peer Y. i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics 2008, 24:127-128. 10.1093/bioinformatics/btm449, 17947255.
32. Cho K, Lim W, Math R, Asraful Islam S, Hong S, Kim H, Yun H. Comparative analysis of the glg operons of Pectobacterium chrysanthemi PY35 and other prokaryotes. J Mol Evol 2008, 67:1-12. 10.1007/s00239-008-9103-7, 18594899.
33. Montero M, Almagro G, Eydallin G, Viale A, Muñoz F, Bahaji A, Li J, Rahimpour M, Baroja-Fernàndez E, Pozueta-Romero J. Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression. Biochem J 2010, 433:107-117.
34. Lin S, Hanson R, Cronan J. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat Chem Biol 2010, 6(9):682-688. 10.1038/nchembio.420, 2925990, 20693992.
35. Rodionov D, Mironov A, Gelfand M. Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res 2002, 12(10):1507-1516. 10.1101/gr.314502, 187538, 12368242.
36. Lemoine F, Lespinet O, Labedan B. Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. BMC Evol Biol 2007, 7:237. 10.1186/1471-2148-7-237, 2238764, 18047665.
37. Gonnet G, Hallett M, Korostensky C, Bernardin L. Darwin v. 2:0: an interpreted computer language for the biosciences. Bioinformatics 2000, 16:101-103. 10.1093/bioinformatics/16.2.101, 10842729.