PhyloPat: Phylogenetic pattern analysis of eukaryotic genes

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Hulsen, Tim ^a   de Vlieg, Jacob ^a,b   Groenen, Peter M A ^b  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b Molecular Design and Informatics   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLETE GENOMES; EUKARYOTIC GENES; FUNCTIONAL INFORMATION; PATTERNS ANALYSIS; PHYLOGENETIC LINEAGES; PHYLOGENETIC TREES; REGULAR EXPRESSIONS; SINGLE LINKAGE CLUSTERING;

CLUSTERING ALGORITHMS; DATABASE SYSTEMS; HTML; PATTERN MATCHING; PROTEINS; QUERY PROCESSING; TOOLS;

GENES;

HOX PROTEIN;

ACCESS TO INFORMATION; ACCURACY; ARTICLE; COMPUTER INTERFACE; CONTROLLED STUDY; EUKARYOTE; EVOLUTION; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC LINKAGE; INFORMATION PROCESSING; INTERNET; ORTHOLOGY; PATTERN RECOGNITION; PHYLOGENETIC TREE; PHYLOGENY; PROTEIN DATABASE; RELIABILITY; SACCHAROMYCES CEREVISIAE; SPECIES DIFFERENCE; ALGORITHM; AUTOMATED PATTERN RECOGNITION; CHROMOSOME MAP; COMPUTER PROGRAM; DATA BASE; DNA SEQUENCE; EUKARYOTIC CELL; GENETICS; INFORMATION RETRIEVAL; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROCEDURES; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

EUKARYOTA;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; CONSERVED SEQUENCE; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; EUKARYOTIC CELLS; INFORMATION STORAGE AND RETRIEVAL; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE;

EID: 33748797415     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-398     Document Type: Article

References (23)

1. Natale DA, Galperin MY, Tatusov RL, Koonin EV: Using the COG database to improve gene recognition in complete genomes. Genetica 2000, 108(1):9-17.
2. Reichard K, Kaufmann M: EPPS: mining the COG database by an extended phylogenetic patterns search. Bioinformatics 2003, 19(6):784-785.
3. Chen F, Mackey AJ, Stoeckert CJJ, Roos DS: OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, 34(Database issue):D363-8.
4. Dehal PS, Boore JL: A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. BMC Bio-informatics 2006, 7:201.
5. Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perriere G: Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 2005, 21(11):2596-2603.
6. Li H, Coghlan A, Ruan J, Coin LJ, Heriche JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R: TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res 2006, 34(Database issue):D572-80.
7. Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez Suarez XM, Flicek P, Graf S, Hammond M, Herrero J, Howe K, lyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ: Ensembl 2006. Nucleic Acids Res 2006, 34(Database issue):DS56-61.
8. Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E: EnsMart: a generic system for fast and flexible access to biological data. Genome Res 2004, 14(1):160-169.
9. Ensembl orthology and paralogy prediction pipeline [http://www.esembl.org/info/data/compara/homology_method.html]
10. Hulsen T, Huynen MA, de Vlieg J, Groenen PM: Benchmarking ortholog identification methods using functional genomics data. Genome Biol 2006, 7(4):R31.
11. Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113.
12. Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52(5):696-704.
13. Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000, 28(1):10-14.
14. Eyre TA, Ducluzeau F, Sneddon TP, Povey S, Bruford EA, Lush MJ: The HUGO Gene Nomenclature Database, 2006 updates. Nucleic Acids Res 2006, 34(Database issue):D319-21.
15. PHYLIP (Phylogeny Inference Package) [http:// evolution.genetics.washington.edu/phylip.html]
16. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29.
17. Al-Shahrour F, Diaz-Uriarte R, Dopazo J: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 2004, 20(4):578-580.
18. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E- TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31(1):374-378.
19. Fredriksson R, Schioth HB: The repertoire of G-protein-coupled receptors in fully sequenced genomes. Mol Pharmacol 2005, 67(5):1414-1425.
20. Korbel JO, Snel B, Huynen MA, Bork P: SHOT: a web server for the construction of genome phylogenies. Trends Genet 2002, 18(3):158-162.
21. Wagner GP, Amemiya C, Ruddle F: Hox cluster duplications and the opportunity for evolutionary novelties. Proc Natl Acad Sci U S A 2003, 100(25):14603-14606.
22. Minguillon C, Gardenyes J, Serra E, Castro LF, Hill-Force A, Holland PW, Amemiya CT, Garcia-Fernandez J: No more than 14: the end of the amphioxus Hox cluster. Int J Biol Sci 2005, 1(1):19-23.
23. PhyloPat lineage PP001723 [http://www.cmbi.ru.nl/pw/phylopat/ phylopat.php?ppid=PP001723]