UNIT 4.3 Using geneid to Identify Genes

  1. Enrique Blanco,
  2. Genís Parra,
  3. Roderic Guigó

Published Online: 1 AUG 2002

DOI: 10.1002/0471250953.bi0403s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Blanco, E., Parra, G. and Guigó, R. 2002. Using geneid to Identify Genes. Current Protocols in Bioinformatics. 4:4.3.

Author Information

  1. Universitat Pompeu Fabra, Barcelona, Spain

Publication History

  1. Published Online: 1 AUG 2002
  2. Published Print: JAN 2003

This is not the most recent version of the article. View current version (1 JUN 2007)


The unit describes the usage of geneid. geneid is a very efficient gene-finding program. It allows for the analysis of large genomic sequences, including whole mammalian chromosomes. These sequences can be partially annotated, and geneid can be used to refine this initial annotation. Parameter configurations exist for a number of eukaryotic species. Geneid produces output in a variety of standard formats. The results, thus, can be processed by a variety of software tools, including visualization programs. Geneid software is in the public domain, and it is undergoing constant development. It is easy to install and use. Exhaustive benchmark evaluations show that geneid compares favorably with other existing gene finding tools.