geneid documentation: 10. geneid history.


Table of contents:
  1. About the authors
  2. geneid versions and names
  3. Acknowledgements
  4. Bibliography
  5. INDEX


About the authors:
Roderic Guigo, Steen Knudsen, Neil Drake and Temple F. Smith contributed to the first implementation of geneid developed at the Molecular Biology Computer Research Resource (Dana Farber Cancer Institute - Hardvard University). It was never distributed , but an e-mail server was latter set up at the Biomolecular Engineering Research Center (Boston University). Kathleen Klose and Steen Knudsen developed the server.

geneid was rewritten from scratch at the Institut Municipal d'Investigacions Mediques in Barcelona in late 1999 mostly by Enrique Blanco and Roderic Guigo. Moises Burset also made some contributions to the code as well as Xavier Messeguer from Universitat Politecnica de Catalunya. This version called geneid v. 1.0 was released in July, 2000.

A new release (2002) called geneid v. 1.1 contained many improvements and fixed bugs. Moreover, a new set of command line options were developed including XML format output, searching ORFs, usage of sequence homology to get better predictions and so on. Processing speed was increased twice while accuraccy of predictions has been maintained.

This latest version geneid v. 1.2 has been released in 2004. New options has been added to support processing of multi-fasta files as well as forcing the prediction of a complete gene in the sequence. New parameter files for more species have been simultaneously delivered with this release.



geneid versions and names:
During many years, geneid has been referred to as GeneID, GeneId, geneID or Geneid. Before release the 1.0 version, we decided for the simplest, most sensible with UNIX commands nomenclature, name: geneid. After that, new releases are enhanced versions of basic 1.0 so that we selected the numeration 1.1 and 1.2.


Acknowledgments:
This work was partially supported by a grant from "Plan nacional de I+D", BIO98-0443-C02-01, and from the "Ministerio de Educacion y Ciencia" (Spain).


Bibliography:
  1. R.Guigo, S.Knudsen, N.Drake and T.F.Smith. Prediction of gene structure. Journal of molecular biology, 226:141-157, 1992.
  2. S.Knudsen, R.Guigo and T.F.Smith. GeneID -- a computer server for prediction of genes in DNA sequences. In H.A.Lim, J.W.Fickett, C.R.Cantor and R.J.Robins, editors, Proceedings on the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis, pages 545-553. World Scientific, 1993.
  3. R.Guigo. Assembling genes from predicted exons in linear time with dynamic programming. Journal of computational biology, 5:681-702, 1998.
  4. G.Parra, E.Blanco and R.Guigo. Geneid in Drosphila. Genome Research 10:511-515, 2000.
  5. E. Blanco, G. Parra and R. Guigó.Using geneid to Identify Genes. In A. D. Baxevanis and D. B. Davison, chief editors: Current Protocols in Bioinformatics. Volume 1, Unit 4.3. John Wiley & Sons Inc., New York, 2002. ISBN: 0-471-25093-7, 2003.




Enrique Blanco Garcia © 2003