Prédiction comparative de gènes

La prédiction comparative de gènes désigne les méthodes de prédiction qui emploient des comparaisons de plusieurs séquences génomiques.

Voici une liste des approches qui, à ma connaissance, ont été publiées au 6 janvier 2003 :

À l'exception de TWINSCAN, tous ces programmes utilisent les conservations de deux séquences génomiques. Le format GFF est utilisé notamment par SGP et EvoGene.

* L'article renvoie vers une adresse qui n'est plus valide.


References

[Bafna and Huson, 2000]
Bafna, V. and Huson, D. (2000). The conserved exon method for gene finding. In ISMB 2000.
[Batzoglou et al., 2000a]
Batzoglou, S., Pachter, L., Mesirov, J., Berger, B., and Lander, E. S. (2000a). Human and mouse gene structure: Comparative analysis and application to exon prediction. In Proceedings of RECOMB, pages 38--47. ACM, New York.
[Batzoglou et al., 2000b]
Batzoglou, S., Pachter, L., Mesirov, J., Berger, B., and Lander, E. S. (2000b). Human and mouse gene structure: Comparative analysis and application to exon prediction. Genome Research, 10:950--958.
[Blayo et al., 2003]
Blayo, P., Rouzé, P., and Sagot, M.-F. (2003). Orphan gene finding - an exon assembly approach. Theoretical Computer Science, 290:1407--1431.
[Kent and Zahler, 2000]
Kent, W. and Zahler, A. (2000). Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Research, 10:1115--1125.
[Korf et al., 2001]
Korf, I., Flicek, P., Duan, D., and Brent, M. (2001). Integrating genomic homology into gene structure prediction. Bioinformatics, 1:S1--S9.
[Meyer and Durbin, 2002]
Meyer, I. and Durbin, R. (2002). Comparative ab initio prediction of gene structures using pair hmms. Bioinformatics, 18:1309--1318.
[Morgenstern et al., 2002]
Morgenstern, B., Rinner, O., Abdeddaïm, S., Haase, D., Mayer, K. F. X., Dress, A., and Mewes, H. (2002). Exon discovery by genomic sequence alignment. Bioinformatics, 18:777--787.
[Novichkov et al., 2001]
Novichkov, P., Gelfand, M., and Mironov, A. (2001). Gene recognition in eukaryotic dna by comparison of genomic sequences. Bioinformatics, 17:1011--1018.
[Parra et al., 2003]
Parra, G., Agarwal, P., Abril, J., Wiehe, T., Fickett, J., and Guigó, R. (2003). Comparative gene prediction in human and mouse. Genome Research, 13:108--117.
[Pedersen and Hein, 2003]
Pedersen, J. and Hein, J. (2003). Gene finding with a hidden markov model of genome structure and evolution. Bioinformatics, 19:219--227.
[Rinner and Morgenstern, 2002]
Rinner, O. and Morgenstern, B. (2002). AGenDA: Gene prediction by comparative sequence analysis. In Silico Biology 2, 0018.
[Taher et al., 2003]
Taher, L., Rinner, O., Garg, S., Sczyrba, A., Brudno, M., Batzoglou, S., and Morgenstern, B. (2003). Agenda: homology-based gene prediction. Bioinformatics, 19:1575--1577.
[Wiehe et al., 2001]
Wiehe, T., Gebauer-Jung, S., Mitchell-Olds, T., and Guigó, R. (2001). SGP-1: Prediction and validation of homologous genes based on sequence alignments. Genome Research, 11:1574--1583.

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Philippe Blayo

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