Wise2 - Documentation

• Wise2 (version 2.1.20 stable) - Wise2 is a package focused on comparisons of biopolymers, commonly DNA sequence and protein sequence. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the FASTA package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers.

• Dynamite (v 1.5a) - Dynamite is a code generating language whose main purpose is to produce efficient code for dynamic programming. Dynamic programming is used throughout sequence analysis in a variety of different guises (sequence alignment, gene prediction etc). Dynamite is used extensively by myself (Ewan Birney), in particular for the Wise2 package.

• GeneWise Probability Appendix - This document describes the derivation of probabilities for the case of an intron of a known phase occuring between two match states. Precisely the same process can be used for the other phase introns and the introns occuring between two insert states or insert to match or match to insert.
  
  
• FTP Download Full Documentation - All documentation relevant to Wise2 is available from our FTP server.
  
  
• Reference
  Ewan Birney, Michele Clamp and Richard Durbin
  GeneWise and Genomewise
  Genome Research 14: 988-995, 2004