Bioinformatics in Colombia: state of the art and perspectives
Keywords:
Computational biology, molecular biology, biotechnology, genomics, Colombia
Abstract
Bioinformatics emerged about 50 years ago, but it was developed greatly during the early 1980's by robust databases such as GenBank, EMBL, and DNA Database of Japan (DDBJ). Bioinformatic routines were rapidly adapted once the main algorithms for sequence analysis became available worldwide. As in other science fields, bioinformatics had minimal impact in low-income countries of Latin America until the last decade.We revised the bioinformatics state of art in Colombia and found a few bioinformatics groups carrying out basic computational biology research. Nowadays, bioinformatics in Colombia has a hopeful scenario thanks to recent science policies adopted by the Colombian Government. Such policies have been adopted in order to establish a new model of sustainable scientific research.
In this brief report we revise the bioinformatics state of the art in Colombia. Finally, we conclude with some considerations for the proposed science model and we describe different perspectives of interest for the Colombian scientific community.
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References
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14. Garnica DP, Pinzón AM, Quesada-Ocampo LM, Bernal AJ, Barreto E, Grunwald NJ, et al. Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus. BMC Genomics. 2006;7:245.
15. Acevedo OE, Lareo LR. Amino acid propensities revisited. OMICS. 2005;9:391-9.
16. Mejía-Guerra MK, Lareo LR. In silico identification of regulatory elements of GRIN1 genes. OMICS. 2005;9:106-15.
17. Sáenz H, Lareo L, Poutou RA, Sosa AC, Barrera LA. Computational prediction of the tertiary structure of the human iduronate 2-sulfate sulfatase. Biomédica. 2007;27:7-20.
18. Ulloa JC, Matiz A, Lareo L, Gutiérrez MF. Molecular analysis of a 348 base-pair segment of open reading frame 2 of human astrovirus. A characterization of Colombian isolates. In Silico Biol. 2005;5:537-46.
19. Narváez G, Lareo L, Rincón J. Mathematical models to correlate molecular topology with substrate affinity of the glycine antagonist in glutamate receptors. Biomédica. 2007;27:116-32.
20. Benítez-Páez A, Cárdenas-Brito S. Dissection of functional residues in receptor activity-modifying proteins through phylogenetic and statistical analyses. Evol Bioinform Online. 2008;4:153-69.
21. Restrepo-Montoya D, Vizcaíno C, Niño LF, Ocampo M, Patarroyo ME, Patarroyo MA. Validating subcellular localization prediction tools with mycobacterial proteins. BMC Bioinformatics. 2009;10:134.
22. Benítez-Páez A. Considerations to improve functional annotations in biological databases. OMICS 2009;13:527-32.
23. Pohlhaus JR, Cook-Deegan RM. Genomics research: world survey of public funding. BMC Genomics. 2008;9:472.
2. Dayhoff M, Schwartz R, Orcutt B. A model of evolutionary change in proteins. En: Atlas of Protein Sequence and Structure. Dayhoff MO, editor. Washington D.C.: National Biomedical Research Foundation-NBR; 1978. p. 345-52.
3. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981;147:195-7.
4. Lipman DJ, Pearson WR. Rapid and sensitive protein similarity searches. Science. 1985;227:1435-41.
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-10.
6. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae.. Science. 1995;269:496-512.
7. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, et al. The complete genome sequence of Escherichia coli K-12. Science. 1997;277:1453-74.
8. Peña MD, Castellanos O, Carrizosa S, Jiménez C, Del Portillo P. La biotecnología, motor de desarrollo para la Colombia de 2015. Bogotá D.C.: Colciencias; 2008.
9. Gutiérrez AJ, Arenas AF, Gómez-Marín JE. Molecular evolution of serine/arginine splicing factors family (SR) by positive selection. In Silico Biol. 2006;6:32.
10. Matute DR, Barreto-Hernández E, Falquet L. Hunting for insect-specific protein domains. In Silico Biol. 2006;6:35-42.
11. Arenas AF, Gutiérrez AJ, Gómez-Marín JE. Evolutionary origin of the protozoan parasites histone-like proteins (HU). In Silico Biol. 2007;8:2.
12. Benítez-Páez A. Sequence analysis of the receptor activity-modifying proteins family, new putative peptides and structural conformation inference. In Silico Biol. 2006;6:467-83.
13. Benítez-Páez A, Cárdenas-Brito S. Dissection of functional residues in receptor activity- modifying proteins through phylogenetic and statistical analyses. Evol Bioinform Online. 2008;4:153-67.
14. Garnica DP, Pinzón AM, Quesada-Ocampo LM, Bernal AJ, Barreto E, Grunwald NJ, et al. Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus. BMC Genomics. 2006;7:245.
15. Acevedo OE, Lareo LR. Amino acid propensities revisited. OMICS. 2005;9:391-9.
16. Mejía-Guerra MK, Lareo LR. In silico identification of regulatory elements of GRIN1 genes. OMICS. 2005;9:106-15.
17. Sáenz H, Lareo L, Poutou RA, Sosa AC, Barrera LA. Computational prediction of the tertiary structure of the human iduronate 2-sulfate sulfatase. Biomédica. 2007;27:7-20.
18. Ulloa JC, Matiz A, Lareo L, Gutiérrez MF. Molecular analysis of a 348 base-pair segment of open reading frame 2 of human astrovirus. A characterization of Colombian isolates. In Silico Biol. 2005;5:537-46.
19. Narváez G, Lareo L, Rincón J. Mathematical models to correlate molecular topology with substrate affinity of the glycine antagonist in glutamate receptors. Biomédica. 2007;27:116-32.
20. Benítez-Páez A, Cárdenas-Brito S. Dissection of functional residues in receptor activity-modifying proteins through phylogenetic and statistical analyses. Evol Bioinform Online. 2008;4:153-69.
21. Restrepo-Montoya D, Vizcaíno C, Niño LF, Ocampo M, Patarroyo ME, Patarroyo MA. Validating subcellular localization prediction tools with mycobacterial proteins. BMC Bioinformatics. 2009;10:134.
22. Benítez-Páez A. Considerations to improve functional annotations in biological databases. OMICS 2009;13:527-32.
23. Pohlhaus JR, Cook-Deegan RM. Genomics research: world survey of public funding. BMC Genomics. 2008;9:472.
How to Cite
1.
Benítez-Páez A, Cárdenas-Brito S. Bioinformatics in Colombia: state of the art and perspectives. biomedica [Internet]. 2010 Aug. 4 [cited 2024 May 16];30(2):170-7. Available from: https://revistabiomedica.org/index.php/biomedica/article/view/180
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Published
2010-08-04
Issue
Section
Essay
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