SimiTri - Visualizing similarity relationships for groups of sequences

Bioinformatics

Volumn 19, Issue 3, 2003, Pages 390-395

  Parkinson, John ^a   Blaxter, Mark ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; DATA ANALYSIS; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC DATABASE; HORIZONTAL GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

CAENORHABDITIS; CAENORHABDITIS ELEGANS;

EID: 0037433041     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/btf870     Document Type: Article

References (18)

1. Altschul,S.F., Gish,W., Miller,W., Myers,M.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Bandi,C., Anderson,T.J.C., Genchi,C. and Blaxter,M. (1998) Phylogeny of Wolbachia in filarial nematodes. Proc. R. Soc. Lond. B, 265, 2407-2413.
4. Blaxter,M.L., DeLey,P., Garey,J.R., Liu,L.X., Scheldeman,P., Vierstraeten,J.R., Mackey,L.Y., Dorris,M., Frisse,L.M., Vida,J.T. and Thomas,W.K. (1998) A molecular evolutionary framework for the phylum Nematoda. Nature, 392, 71-75.
5. Blaxter,M.L., Daub,J., Guiliano,D., Parkinson,J. and Whitton,C. (2002) The Brugia malayi genome project: expressed sequence tags and gene discovery. Trans. R. Soc. Trop. Med. Hyg., 96, 7-17.
6. Daubin,V., Gouy,M. and Perriere,G. (2002) A phylogenetic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res., 12, 1080-1090.
7. Glasner,J.D., Kocher,T.D. and Collins,J.J. (1995) Caenorhabditis elegans contains genes encoding two new members of the Zn-containing alcohol dehydrogenase family. J. Mol. Evol., 41, 46-53.
8. Koski,L.B. and Golding,G.B. (2001) The closest BLAST hit is often not the nearest neighbour. J. Mol. Evol., 52, 540-542.
9. Maizels,R.M., Blaxter,M.L. and Scott,A. (2001) Immunological genomics of Brugia malayi: filarial genes implicated in immune evasion and protective immunity. Parasite Immunol., 23, 327-344.
10. Matte-Tailliez,O., Brochier,C., Forterre,P. and Philippe,H. (2002) Archaeal phylogeny based on ribosomal proteins. Mol. Biol. Evol., 19, 631-639.
11. Mushegian,A.R., Garey,J.R., Martin,J. and Liu,L.X. (1998) Large-scale taxonomic profiling of eukaryotic model organisms: a comparison of orthologous proteins encoded by the human, fly, nematode, and yeast genomes. Genome Res., 8, 590-598.
12. Parkinson,J., Whitton,C., Guiliano,D., Daub,J. and Blaxter,M.L. (2001) 200 000 nematode expressed sequence tags on the net. Trends Parasit., 17, 394-396.
13. Parkinson,J., Guiliano,D. and Blaxter,M.L. (2002) Making sense of EST sequences by CLOBBing them. BMC Bioinf., 3, 31.
14. Sicheritz-Ponten,T. and Andersson,S.G.E. (2001) A phylogenomic approach to microbial evolution. Nucleic Acids Res., 29, 545-552.
15. Swofford,D.L. (2000) PAUP* (Phylogenetic Analysis using Parsimony and Other Methods), Version 4.10, Sinauer Associates, Sunderland, MA.
16. The C. elegans SequencingConsortium (1998) Genome sequence of the nematode C.elegans: a platform for investigating biology. Science, 282, 2012-2018.
17. Wood,V., William,R.G., Rajandream,M.A., Lyne,M., Stewart,A. et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature, 415, 871-880.
18. Xie,T. and Ding,D. (2000) Investigating 42 candidate orthologous protein groups by molecdular evolutionary analysis on genome scale. Gene, 261, 305-310.