UNIT 4.8 Using TWINSCAN to Predict Gene Structures in Genomic DNA Sequences

  1. Ping Hu,
  2. Michael R. Brent

Published Online: 1 NOV 2003

DOI: 10.1002/0471250953.bi0408s03

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Hu, P. and Brent, M. R. 2003. Using TWINSCAN to Predict Gene Structures in Genomic DNA Sequences. Current Protocols in Bioinformatics. 4:4.8.

Author Information

  1. Washington University, St. Louis, Missouri

Publication History

  1. Published Online: 1 NOV 2003
  2. Published Print: SEP 2003

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


TWINSCAN is a gene-prediction system that combines the methods of ab initio predictors like GENSCAN with information derived from genome comparison. This unit describes the use of TWINSCAN to identify gene structures in eukaryotic genomic sequences. Protocols for using TWINSCAN through its Web interface and from the command line in a Linux environment are provided. Detailed discussion about the appropriate parameter settings, input sequence processing, and choice of genome for comparison are included.


  • gene prediction;
  • sequence alignment;
  • comparative genome analysis;
  • cross-species sequence comparison;
  • genome annotation