geneid documentation: 9. geneid history.

Table of contents:

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.

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

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. As this new release is an enhanced version of 1.0., we selected the number 1.1..

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).

  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.

Enrique Blanco Garcia © 2001