Genewise

From the Wise2 website documentation:

" Wise2 is a package focused on comparisons of bio polymers, 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 bio polymers. "

" Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment. There is currently no other package that I know of that contains this type of algorithm with a full blown gene prediction model and a hidden Markov model of a protein domain. "

" Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul's generalised gap penalties, or even experimental ones developed in house, such as dba (see section 7.1). The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2. "

Installed on: Opteron cluster.

Usage on the Opteron cluster

Wise2 users will find it convenient to use the /biomed/lib/examples/.login.fixed login file. It adds to your default path directories where many sequence analysis packages are stored, sets up the environment for EMBOSS, and defines some environment variables for sequence analysis packages.

These executables are found in /biomed/src/Wise2/wise2.1.23c/bin, and are defined for you if you use the .fixed.login file.

    dba dnal estwise estwisedb genewise genewisedb psw pswdb

Documentation

The Genewise documentation is found at http://www.ebi.ac.uk/Wise2/doc_wise2.html.

See also