UNIT 4.3 Using geneid to Identify Genes

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

Published Online: 1 JUN 2007

DOI: 10.1002/0471250953.bi0403s18

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Blanco, E., Parra, G. and Guigó, R. 2007. Using geneid to Identify Genes. Current Protocols in Bioinformatics. 18:4.3:4.3.1–4.3.28.

Author Information

  1. Centre de Regulació Genòmica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Barcelona, Spain

Publication History

  1. Published Online: 1 JUN 2007
  2. Published Print: JUN 2007


This unit describes the usage of geneid, an efficient gene-finding program that 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. Training geneid is relatively easy, and 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.


  • Gene identification;
  • genes;
  • exons;
  • splicing;
  • genome annotation;
  • bioinformatics