Exploring the genome of Trypanosoma vivax through GSS and in silico comparative analysis

OMICS A Journal of Integrative Biology

Volumn 9, Issue 1, 2005, Pages 116-128

  Guerreiro, Luana Tatiana A ^a   Souza, Silvana S ^a   Wagner, Glauber ^a   De Souza, Edson A ^b   Mendes, Pablo N ^c   Campos, Linair M ^c   Barros, Lígia ^c   Pires, Paulo F ^c   Campos, Maria Luiza M ^c   Grisard, Edmundo C ^b   Dávila, Alberto M R ^a  

^a INSTITUTO OSWALDO CRUZ   (Brazil)

^b FEDERAL UNIVERSITY OF SANTA CATARINA   (Brazil)

^c FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

COMPARATIVE STUDY; COMPUTER MODEL; DATA BASE; DIAGNOSTIC TEST; GENBANK; GENE SEQUENCE; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; TRYPANOSOMA VIVAX;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENES, PROTOZOAN; GENETIC MARKERS; GENOME, PROTOZOAN; OPEN READING FRAMES; POLYMERASE CHAIN REACTION; PROTOZOAN PROTEINS; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRYPANOSOMA VIVAX;

EID: 20244362657     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2005.9.116     Document Type: Review

References (22)

1. AGUERO, F., VERDUN, R.E., FRASCH, A.C., et al. (2000). A random sequencing approach for the analysis of the Trypanosoma cruzi genome: general structure, large gene and repetitive DNA families, and gene discovery. Gen Res 10, 1996-2005.
2. AKOPYANTS, N.S., CLIFTON, S.W., MARTIN, J., et al. (2001). A survey of the Leishmania major Friedlin strain V1 genome by shotgun sequencing: a resource for DNA microarrays and expression profiling. Mol Biochem Parasitol 113, 337-340.
3. ALTSCHUL, S.F., MADDEN, T.L., SCHfFFER, A.A., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 25, 3389-3402.
4. CARVER, T., and BLEASBY, A. (2003). The design of Jemboss: a graphical user interface to EMBOSS. Bioinformatics 19, 1837-1843.
5. DÁVILA, A.M.R., and SILVA, R.A. (2000). Animal trypanosomosis in South America. Current status, partnership, and information technology. Ann NY Acad Sci 916, 199-212.
6. DEANE, M.P., MANGIA, R.H., PEREIRA, N.M., et al. (1984). Trypanosoma cruzi: strain selection by different schedules of mouse passage of an initially mixed infection. Mem Inst Oswaldo Cruz. 79, 495-497.
7. DELCHER, A.L., HARMON, D., KASIF, S., et al. (1999). Improved microbial gene identification with GLIMMER. Nucleic Acid Res 27, 4636-4641.
8. DJIKENG, A., AGUFA, C., DONELSON, J.E., et al. (1998). Generation of expressed sequence tags as physical landmarks in the genome of Trypanosoma brucei. Gene 221, 93-106.
9. EL-SAYED, N.M., and DONELSON, J.E. (1997). A survey of the Trypanosoma brucei rhodesiense genome using shotgun sequencing. Mol Biochem Parasitol 84, 167-78.
10. EWING, B., HILLIER, L., WEND, M.C., et al. (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8, 175-185.
11. EWING, B., and GREEN, P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8, 186-194.
12. GARDINER, P.R. (1989). Recent studies of the biology of Trypanosoma vivax. Adv Parasitol 28, 229-317.
13. HANNAERT, V., SAAVEDRA, E., DUFFIEUX, F., et al. (2003). Plant-like traits associated with metabolism of Trypanosoma parasites. Proc Natl Acad Sci USA 100, 1067-1071.
14. HUANG, X., and MADAN, A. (1999). CAP3: a DNA sequence assembly program. Genome Res 9, 868-877.
15. JONES, T.W., and DÁVILA, A.M. (2001). Trypanosoma vivax-out of Africa. Trends Parasitol 17, 99-101.
16. KIELISZEWSKI, M.J., and LAMPORT, D.T. (1994). Extensin: repetitive motifs, functional sites, post-translational codes, and phylogeny. Plant J 5, 157-72.
17. LOWE, T.M., and EDDY, S.R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acid Res 25, 955-964.
18. OTIGBUO, I.N., and OYERINDE, J.P. (1993). A modified medium for the in vitro cultivation of trypanosomes. Afr J Med Med Sci 22, 63-71.
19. SAMBROOK, J., and RUSSEL, D.W. (2001). Molecular Cloning: A Laboratory Manual, Vol. 2, 3rd ed. (CSHL Press, New York).
20. SEIDL, A., DAVILA, A.M, and SILVA, R.A. (1999). Estimated financial impact of Trypanosoma vivax on the Brazilian pantanal and Bolivian lowlands. Mem Inst Oswaldo Cruz 94, 269-72.
21. WALLER, R.F., McCONVILLE, M.J., and McFADDEN, G.I. (2004). More plastids in human parasites? Trends Parasitol 20, 54-7.
22. WICKSTEAD, B., ERSFELD, K., and GULL, K. (2004). The small chromosomes of Trypanosoma brucei involved in antigenic variation are constructed around repetitive palindromes. Genome Res 14, 1014-1024.