Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Boekhorst, Jos ^a   Snel, Berend ^a,b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY BIOLOGY; FUNCTIONAL ANNOTATION; GENOMIC INFORMATION; HOMOLOGOUS PROTEINS; PRIMARY SEQUENCES; PROTEIN SEQUENCES; SEQUENCE SIMILARITY; TERTIARY STRUCTURES;

BIOLOGY;

GENES;

BACTERIAL PROTEIN; HYBRID PROTEIN; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; COMPUTER PROGRAM; CONTROLLED STUDY; GENE ORDER; GENETIC SIMILARITY; NONHUMAN; SEQUENCE HOMOLOGY; STRUCTURAL BIOINFORMATICS; STRUCTURAL GENOMICS; CHEMISTRY; INFORMATION RETRIEVAL; METHODOLOGY; MOLECULAR GENETICS; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; DATABASES, PROTEIN; INFORMATION STORAGE AND RETRIEVAL; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 35648986069     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-356     Document Type: Article

References (26)

1. Koonin EV Orthologs, paralogs, and evolutionary genomics Annu Rev Genet 2005, 39:309-338. 10.1146/annurev.genet.39.073003.114725 16285863
2. Copley RR Goodstadt L Ponting C Eukaryotic domain evolution inferred from genome comparisons Curr Opin Genet Dev 2003, 13(6):623-628. 10.1016/ j.gde.2003.10.004 14638325
3. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215(3):403-410. 2231712
4. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25(17):3389-3402. 146917 9254694 10.1093/nar/25.17.3389
5. Eddy SR Profile hidden Markov models Bioinformatics 1998, 14(9):755-763. 10.1093/bioinformatics/14.9.755 9918945
6. Sridhar J Rafi ZA Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention Omics 2007, 11(1):74-99. 10.1089/ omi.2006.0006 17411397
7. Tatusov RL Fedorova ND Jackson JD Jacobs AR Kiryutin B Koonin EV Krylov DM Mazumder R Mekhedov SL Nikolskaya AN Rao BS Smirnov S Sverdlov AV Vasudevan S Wolf YI Yin JJ Natale DA The COG database: An updated version includes eukaryotes BMC Bioinformatics 2003, 4:41. 222959 12969510 10.1186/1471-2105-4-41
8. Kursula P Ojala J Lambeir AM Wierenga RK The catalytic cycle of biosynthetic thiolase: A conformational journey of an acetyl group through four binding modes and two oxyanion holes Biochemistry 2002, 41(52):15543-15556. 10.1021/bi0266232 12501183
9. Huynen MA Snel B Bork P Inversions and the dynamics of eukaryotic gene order Trends Genet 2001, 17(6):304-306. 10.1016/S0168-9525(01)02302-2 11377779
10. Dandekar T Snel B Huynen M Bork P Conservation of gene order: A fingerprint of proteins that physically interact Trends Biochem Sci 1998, 23(9):324-328. 10.1016/S0968-0004(98)01274-2 9787636
11. Overbeek R Fonstein M D'Souza M Pusch GD Maltsev N The use of gene clusters to infer functional coupling Proc Natl Acad Sci U S A 1999, 96(6):2896-2901. 15866 10077608 10.1073/pnas.96.6.2896
12. Coin L Bateman A Durbin R Enhanced protein domain discovery using taxonomy BMC Bioinformatics 2004, 5:56. 434490 15137915 10.1186/ 1471-2105-5-56
13. Sadreyev R Grishin N COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance J Mol Biol 2003, 326(1):317-336. 10.1016/S0022-2836(02)01371-2 12547212
14. Soding J Protein homology detection by HMM-HMM comparison Bioinformatics 2005, 21(7):951-960. 10.1093/bioinformatics/bti125 15531603
15. Coin L Bateman A Durbin R Enhanced protein domain discovery by using language modeling techniques from speech recognition Proc Natl Acad Sci U S A 2003, 100(8):4516-4520. 404693 12668763 10.1073/pnas.0737502100
16. Griffiths E Ventresca MS Gupta RS BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species BMC Genomics 2006, 7:14. 1403754 16436211 10.1186/1471-2164-7-14
17. Hartman H Fedorov A The origin of the eukaryotic cell: A genomic investigation Proc Natl Acad Sci U S A 2002, 99(3):1420-1425. 122206 11805300 10.1073/pnas.032658599
18. Makarova K Slesarev A Wolf Y Sorokin A Mirkin B Koonin E Pavlov A Pavlova N Karamychev V Polouchine N Shakhova V Grigoriev I Lou Y Rohksar D Lucas S Huang K Goodstein DM Hawkins T Plengvidhya V Welker D Hughes J Goh Y Benson A Baldwin K Lee JH Diaz-Muniz I Dosti B Smeianov V Wechter W Barabote R Lorca G Altermann E Barrangou R Ganesan B Xie Y Rawsthorne H Tamir D Parker C Breidt F Broadbent J Hutkins R O'Sullivan D Steele J Unlu G Saier M Klaenhammer T Richardson P Kozyavkin S Weimer B Mills D Comparative genomics of the lactic acid bacteria Proc Natl Acad Sci U S A 2006, 103(42):15611-15616. 1622870 17030793 10.1073/pnas.0607117103
19. Finn RD Mistry J Schuster-Bockler B Griffiths-Jones S Hollich V Lassmann T Moxon S Marshall M Khanna A Durbin R Eddy SR Sonnhammer EL Bateman A Pfam: Clans, web tools and services Nucleic Acids Res 2006, 34 Database issue D247-51. 1347511 16381856 10.1093/nar/gkj149
20. Murzin AG Brenner SE Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures J Mol Biol 1995, 247(4):536-540. 10.1006/jmbi.1995.0159 7723011
21. Gardner MJ Hall N Fung E White O Berriman M Hyman RW Carlton JM Pain A Nelson KE Bowman S Paulsen IT James K Eisen JA Rutherford K Salzberg SL Craig A Kyes S Chan MS Nene V Shallom SJ Suh B Peterson J Angiuoli S Pertea M Allen J Selengut J Haft D Mather MW Vaidya AB Martin DM Fairlamb AH Fraunholz MJ Roos DS Ralph SA McFadden GI Cummings LM Subramanian GM Mungall C Venter JC Carucci DJ Hoffman SL Newbold C Davis RW Fraser CM Barrell B Genome sequence of the human malaria parasite Plasmodium falciparum Nature 2002, 419(6906):498-511. 10.1038/ nature01097 12368864
22. Koonin EV Eugene V. Koonin (Interview) Curr Biol 2004, 14(3):R96-7. 10.1016/S0960-9822(04)00025-9 14986627
23. Benson DA Karsch-Mizrachi I Lipman DJ Ostell J Wheeler DL GenBank Nucleic Acids Res 2006, 34 Database issue D16-20. 1347519 16381837 10.1093/nar/gkj157
24. Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 2004, 32(5):1792-1797. 390337 15034147 10.1093/nar/gkh340
25. Guindon S Gascuel O A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520 14530136
26. Page RD TreeView: An application to display phylogenetic trees on personal computers Comput Appl Biosci 1996, 12(4):357-358. 8902363