Tehdyt toimenpiteet
Wise2 at CSC
Versions
- Wise2.2.0 software package is available in Hippu.
Description
Wise2 program contains tools for comparing protein sequences and protein profile HMMs to nucleotide sequences. Wise2 programs utilize structural gene models that enable it to cope with introns and farme shift errors.
Wise2 programs
| Program | Description |
|---|---|
| Main wise2 programs |
|
| genewise | Aligns a genomic nucleotide sequence with a protein sequence or a protein profile HMM |
| genewisedb |
Compares a genomic nucleotide sequence agaist a set of protein sequences or protein profile HMMs |
| estwise | Aligns a cDNA sequence with a protein sequence or profile HMM |
| estwisedb | Compares a cDNA nucleotide sequence agaist a set of protein sequences or protein profile HMMs |
| Other wise2 programs |
|
| dba |
Dna Block Aligner |
| psw | Protein Smith-Waterman and other comparisons |
| pswdb | protein smith waterman database searching |
Using Wise2 in Hippu
The wise2 package is taken in use together with the HMMER package. The setup command is:
module load wise2
After the setup command, Hippu recognizes Wise2 commands. Also an environment variable HMMERDB is defined to point to the Pfam databases.
You can list the command line options of Wise2 programs by using option -help. For example:
genewise -help
A simple comparison between a nucleotide and a protein sequece can be done with following command:
genewise protein.fasta nucleotide.fasta
Pfam database
In Hippu, you can use Pfam_ls and Pfam_fs databases with Wise2 commands. For example comparing an EST sequence against a Pfam_fs HMM-database can be performed with command:
estwisedb -pfam $HMMERDB/Pfam_fs -dnadb ESTs.fasta > results.txt
