Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis

Bioinformatics

Volumn 24, Issue 13, 2008, Pages

  Vaughan, Ashley ^a   Chiu, Sum Ying ^b   Ramasamy, Gowthaman ^a   Li, Ling ^a   Gardner, Malcolm J ^a   Tarun, Alice S ^a   Kappe, Stefan H I ^a,b   Peng, Xinxia ^a  

^a SEATTLE BIOMEDICAL RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PROTOZOAL DNA;

ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; DATA ANALYSIS; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DATABASE; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PLASMODIUM (LIFE CYCLE STAGE); PLASMODIUM FALCIPARUM; PLASMODIUM YOELII; PRIORITY JOURNAL; PROTEOMICS; SEQUENCE ANALYSIS; SPECIES COMPARISON; UNINDEXED SEQUENCE;

PLASMODIUM FALCIPARUM; PLASMODIUM YOELII; PLASMODIUM YOELII YOELII; RODENTIA;

BLOOD; DISEASES; INTELLIGENT SYSTEMS; MOLECULAR BIOLOGY;

ANNOTATED GENES; ASSESSMENT AND IMPROVEMENT; COMPARATIVE ANALYSIS; GENE PREDICTION; GENOME ANNOTATION; MALARIA PARASITE; PROTEOMIC ANALYSIS; SYSTEMATIC ASSESSMENT;

GENES;

EID: 46249120670     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn140     Document Type: Article

References (28)

1. Bendtsen,J.D. et al. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340, 783-795.
2. Blair,P.L. and Carucci,D.J. (2005) Functional proteorne and expression analysis of sporozoites and hepatic stages of malaria development. Curr. Top. Microbiol. Immunol., 295, 417-438.
3. Brejova,B. et al. (2005) ExonHunter: A comprehensive approach to gene finding. Bioinformatics, 21(Suppl. 1), i57-i65.
4. Carlton,J.M. et al. (2002) Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature, 419, 512-519.
5. Eng,J.K. et al. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am Soc. Mass Spect., 5, 976-989.
6. Gardner,M.J. et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419, 498-511.
7. Hall,N. et al. (2005) A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science, 307, 82-86.
8. Kaiser,K. et al. (2004) Differential transcriptome profiling identifies Plasmodium genes encoding pre-erythrocytic stage-specific proteins. Mol. Microbiol., 51, 1221-1232.
9. Kariu,T. et al. (2006) CelTOS, a novel malarial protein that mediates transmission to mosquito and vertebrate hosts. Mol. Microbiol., 59, 1369-1379.
10. Keller,A. et al. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem., 74, 5383-5392.
11. Kooij,T.W. et al. (2005) A Plasmodium whole-genome synteny map: Indels and synteny breakpoints as foci for species-specific genes. PLoS Pathogens, 1, e44.
12. Krogh,A. et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol., 305, 567-580.
13. Kumar,K.A. et al. (2006) The circumsporozoite protein is an immunodominant protective antigen in irradiated sporozoites. Nature 444, 937-940.
14. Li,L. et al. (2003) Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database. Genome Res., 13, 443-454.
15. Lu,F. et al. (2007) cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genomics, 8, 255.
16. Luke,T.C. and Hoffman,S.L. (2003) Rationale and plans for developing a non-replicating, metabolically active, radiation-attenuated Plasmodium falciparum sporozoite vaccine. J. EXperi. Biol., 206, 3803-3808.
17. Mulder,N.J. et al. (2007) New developments in the InterPro database. Nucleic Acids Res., 35, D224-D228.
18. Pertea,G. et al. (2003) TIGR Gene Indices clustering tools (TGICL): A software system for fast clustering of large EST datasets. Bioinformatics, 19, 651-652.
19. Rice,P. et al. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
20. Roy,S.W. and Hartl,D.L. (2006) Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number. Genome Res., 16, 750-756.
21. Sacci,J.B. Jr. et al. (2005) Transcriptional analysis of in vivo Plasmodium yoelii liver stage gene expression. Mol. Biochem. Parasitol., 142, 177-183.
22. Salzberg,S.L. (2007) Genome re-annotation: A WIKI solution?, Genome Biol., 8, 102.
23. Slater,G.S. and Birney,E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
24. Snow,R.W. et al. (2005) The global distribution of clinical episodes of Plasmodium falciparum malaria. Nature, 434 214-217.
25. Tarun,A.S. et al. (2006) Quantitative isolation and in vivo imaging of malaria parasite liver stages. Int. J. Parasitol., 36, 1283-1293.
26. Tarun,A.S. et al. (2008) A combined transcriptome and proteome survey of malaria parasite liver stages. Proc. Natl Acad. Sci. USA 105, 305-310.
27. Tatusov,R.L. et al. (1997) A genomic perspective on protein families. Science, 278, 631-637.
28. Wang,Q. et al. (2004) Transcriptome of axenic liver stages of Plasmodium yoelii. Mol. Biochem. Parasitol., 137, 161-168.