UNIT 4.8 Using N-SCAN or TWINSCAN to Predict Gene Structures in Genomic DNA Sequences

  1. Marijke J. van Baren,
  2. Brian C. Koebbe,
  3. Michael R. Brent

Published Online: 1 DEC 2007

DOI: 10.1002/0471250953.bi0408s20

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

van Baren, M. J., Koebbe, B. C. and Brent, M. R. 2007. Using N-SCAN or TWINSCAN to Predict Gene Structures in Genomic DNA Sequences. Current Protocols in Bioinformatics. 20:4.8:4.8.1–4.8.16.

Author Information

  1. Washington University, St. Louis, Missouri

Publication History

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


N-SCAN is a gene-prediction system that combines the methods of ab initio predictors like GENSCAN with information derived from genome comparison. It is the latest in the TWINSCAN series of programs. This unit describes the use of N-SCAN to identify gene structures in eukaryotic genomic sequences. Protocols for using N-SCAN 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. Curr. Protoc. Bioinform. 20:4.8.1-4.8.16. © 2007 by John Wiley & Sons, Inc.


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