Unit
UNIT 4.8 Using N-SCAN or TWINSCAN to Predict Gene Structures in Genomic DNA Sequences
Published Online: 1 DEC 2007
DOI: 10.1002/0471250953.bi0408s20
Copyright © 2007 by John Wiley and Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
Additional Information
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.
Publication History
- Published Online: 1 DEC 2007
- Published Print: DEC 2007
Abstract
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.
Keywords:
- N-SCAN;
- TWINSCAN;
- gene prediction;
- sequence alignment;
- comparative genome analysis;
- cross-species sequence comparison ;
- genome annotation
