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

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.