OrthoClusterDB: An online platform for synteny blocks

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Ng, Man Ping ^a   Vergara, Ismael A ^a   Frech, Christian ^a   Chen, Qingkang ^a   Zeng, Xinghuo ^a   Pei, Jian ^a   Chen, Nansheng ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE GENOMICS; FULL CONTROL; GENE CLUSTERS; GENOME SEQUENCES; ONLINE PLATFORMS; PUBLIC DATABASE; SYNTENY BLOCKS; TECHNOLOGICAL ADVANCES;

E-LEARNING; VISUALIZATION;

GENES;

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; CAENORHABDITIS ELEGANS; CHROMOSOME; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC DATABASE; GENOMICS; INTERNET; NONHUMAN; ONLINE SYSTEM; PSEUDOMONAS AERUGINOSA; GENOME; METHODOLOGY; SYNTENY;

EUKARYOTA;

DATABASES, GENETIC; GENOME; GENOMICS; INTERNET; SOFTWARE; SYNTENY; USER-COMPUTER INTERFACE;

EID: 67650961327     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-192     Document Type: Article

References (19)

1. Blumenthal T Evans D Link CD Guffanti A Lawson D Thierry-Mieg J Thierry-Mieg D Chiu WL Duke K Kiraly M A global analysis of Caenorhabditis elegans operons Nature 2002, 6891:851-853. 10.1038/ nature00831 12075352
2. Jacob F Operon: A group of genes with the expression coordinated by an operator C R Hebd Seances Acad Sci 1960, 250:1727-1729. 14406329
3. Johnnidis J Venanzi E Taxman D JP T CO B DJ M Chromosomal clustering of genes controlled by the aire transcription factor Proc Natl Acad Sci USA 2005, 102(20):7233-7238. 1129145 15883360 10.1073/pnas.0502670102
4. Roy J Stuart J Lund J Stuart K Chromosomal clustering of muscle-expressed genes in C. elegans Nature 2002, 418:975-979. 12214599
5. Hardison RC Comparative genomics PLoS biology 2003, 1(2):E58. 261895 14624258 10.1371/journal.pbio.0000058
6. Passarge E Horsthemke B Farber RA Incorrect use of the term synteny Nature genetics 1999, 23(4):387. 10.1038/70486 10581019
7. Pevzner P Tesler G Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes Genome Res 2003, 13(1):37-45. 430962 12529304 10.1101/gr.757503
8. Gregory SG Sekhon M Schein J Zhao S Osoegawa K Scott CE Evans RS Burridge PW Cox TV Fox CA A physical map of the mouse genome Nature 2002, 418(6899):743-750. 10.1038/nature00957 12181558
9. Margulies EH Birney E Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes Nat Rev Genet 2008, 9(4):303-313. 10.1038/nrg2185 18347593
10. Zeng X Pei J Vergara IA Nesbitt M Wang K Chen N OrthoCluster: A new tool for mining synteny blocks and applications in comparative genomics 11th International Conference on Extending Technology (EDBT), March 25-30, 2008: 2008; Nantes, France 2008
11. Sinha AU Meller J Cinteny: Flexible analysis and visualization of synteny and genome rearrangements in multiple organisms BMC Bioinformatics 2007, 8:82. 1821339 17343765 10.1186/1471-2105-8-82
12. Soderlund C Nelson W Shoemaker A Paterson A SyMAP: A system for discovering and viewing syntenic regions of FPC maps Genome Res 2006, 16(9):1159-1168. 1557773 16951135 10.1101/gr.5396706
13. Stover CK Pham XQ Erwin AL Mizoguchi SD Warrener P Hickey MJ Brinkman FS Hufnagle WO Kowalik DJ Lagrou M et al Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen Nature 2000, 406(6799):959-964. 10.1038/35023079 10984043
14. Stein LD Mungall C Shu S Caudy M Mangone M Day A Nickerson E Stajich JE Harris TW Arva A et al The generic genome browser: A building block for a model organism system database Genome Res 2002, 12(10):1599-1610. 187535 12368253 10.1101/gr.403602
15. Remm M Storm CE Sonnhammer EL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons Journal of molecular biology 2001, 314(5):1041-1052. 10.1006/jmbi.2000.5197 11743721
16. Alexeyenko A Tamas I Liu G Sonnhammer EL Automatic clustering of orthologs and inparalogs shared by multiple proteomes Bioinformatics (Oxford, England) 2006, 22(14):e9-15. 10.1093/bioinformatics/btl213 16873526
17. Chen N Harris TW Antoshechkin I Bastiani C Bieri T Blasiar D Bradnam K Canaran P Chan J Chen CK et al WormBase: A comprehensive data resource for Caenorhabditis biology and genomics Nucleic acids research 2005, 33(Database):D383-389. 540020 15608221
18. Crosby MA Goodman JL Strelets VB Zhang P Gelbart WM FlyBase: Genomes by the dozen Nucleic acids research 2007, 35(Database):D486-491. 1669768 17099233 10.1093/nar/gkl827
19. Flicek P Aken BL Beal K Ballester B Caccamo M Chen Y Clarke L Coates G Cunningham F Cutts T et al Ensembl 2008 Nucleic acids research 2008, 36(Database):D707-714. 2238821 18000006