A graphical tool for parasite genome annotation

Computer Methods and Programs in Biomedicine

Volumn 73, Issue 1, 2004, Pages 55-60

  Nilsson, Daniel ^a   Andersson, Björn ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Annotation; Gene prediction; Kinetoplastid; Parasite genomics; Visualisation

Indexed keywords

COMPUTER SOFTWARE; DATABASE SYSTEMS; DECISION SUPPORT SYSTEMS; GENES;

GRAPHICAL TOOLS;

BIOMEDICAL ENGINEERING;

ARTICLE; CALCULATION; COMPUTER PROGRAM; DATA BASE; DECISION MAKING; GENE SEQUENCE; GENOME; LABORATORY; NONHUMAN; PARASITE; PREDICTION; PROKARYOTE; PROTOZOON; TRYPANOSOMA CRUZI;

EID: 0347356238     PISSN: 01692607     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-2607(02)00162-1     Document Type: Article

References (28)

1. Degrave W.M., Melville S., Ivens A., Aslett M. Parasite genome initiatives. International Journal for Parasitology. 31:2001;532-536.
2. Harris N.L. Genotator: a workbench for sequence annotation. Genome Research. 7:(7):1997;754-762.
3. Sakata K., Nagamura Y., Numa H., Antonio B., Nagasaki H., Idonuma A., Watanabe W., Shimizu Y., Horiuchi I., Matsumoto T., Sasaki T., Higo K. RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Research. 30:(1):2002;98-102.
4. Glusman G., Lancet D. GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses. Bioinformatics. 16:(5):2000;482-483.
5. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.-A., Barrell B. Artemis: sequence visualisation and annotation. Bioinformatics. 10:(16):2000;944-945.
6. Pearson W.R., Lipman D.J. Improved tools for biological sequence comparison. Proceedings of National Academy of Science USA. 85:(8):1988;2444- 2448.
7. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A., Wheeler D.L. Genbank. Nucleic Acids Research. 30:(1):2002;17-20.
8. Salzberg S., Delcher A., Kasif S., White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Research. 26:(2):1997;544-548.
9. Fickett J. Recognition of protein coding regions in DNA sequences. Nucleic Acids Research. 26:(2):1982;544-548.
10. Altschul S., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. Journal of Molecular Biology. 215:1990;403-410.
11. Altschul S., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 25:(17):1997;3389-3402.
12. Mair G., Shi H., Li H., Djikeng A., Aviles H., Bishop J., Falcone F., Gavrilescu C., Montgomery J., Santori M., Stern L., Wang Z., Ullu E., Tschudi C. A new twist in trypanosome RNA metabolism: cis-splicing of pre-mRNA. RNA. 6:2000;163-169.
13. C.E. Shannon, A mathematical theory of communication, Bell System Technical Journal 27 (1948) 379-423, 623-656.
14. Frank A., Lobry J. Assymetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene. 238:1999;65-67.
15. F. Blattner, G. III Plunket, C. Bloch, N. Perna, V. Burland, M. Riley, J. Collado-Vides, J. Glasner, C. Rode, G. Mayhew, J. Gregor, N. Davis, H. Kirkpatrick, M. Goeden, D. Rose, B. Mau, Y. Shao, The complete genome sequence of Escherichia coli K-12, Science 277 (5331) (1997) 1453-1474.
16. McDonagh P.D., Myler P.J., Stuart K. The unusual gene organization of Leishmania major chromosome 1 may reflect novel transcription processes. Nucleic Acids Research. 28:(14):2000;2800-2803.
17. Baldi P., Baisnée P.-F. Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics. 16:(10):2000;865-889.
18. El-Sayed N.M., Hegde P., Quackenbush J., Melville S.E., Donelson J.E. The African trypanosome genome. International Journal for Parasitology. 30:2000;329-345.
19. Andersson B., Åslund L., Tammi M., Tran A.-N., Hoheisel J.D., Pettersson U. Complete Sequence of a 93.4-kb Contig from Chromosome 3 of Trypanosoma cruzi containing a strand-switch region. Genome Research. 8:1998;809-816.
20. Myler P., Sisk E., McDonagh P., Martinez-Calvillo S., Schnaufer A., Sunkin S., Yan S., Madhubala R., Ivens A., Stuart K. Genomic organization and gene function in Leishmania. Biochemical Society Transactions. 28:(5):2000;527-531.
21. Murakami K., Takagi T. Gene recognition by combination of several gene-finding programs. Bioinformatics. 14:(8):1998;665-675.
22. Pavlovic V., Garg A., Kasif S. A bayesian framework for combining gene predictions. Bioinformatics. 18:(1):2002;19-27.
23. NCBI ASN.1, http://www.ncbi.nlm.nih.gov/Sitemap/Summary/asn1.html (October 2001).
24. Sequin, http://www.ncbi.nlm.nih.gov/Sequin/ (August 2001).
25. Wall L., Schwartz R. Programming Perl. 1991;O'Reilly and Associates, Sebastopol, CA.
26. N. Ing-Simmons, Perl/Tk Tk GUI Toolkit for perl5, Can be found at any CPAN mirror; e.g. ftp://ftp.cpan.org/CPAN/authors/id/NI-S/ (August 2001).
27. BioPerl, http://bioperl.org (February 2002).
28. R. Durbin, D. Haussler, L. Stein, S. Lewis, A. Krogh, et al., GFF: an Exchange Format for Feature Description, http://www.sanger.ac.uk/Software/ formats/GFF/ (November 2002).