Provean 1.1.3: Difference between revisions
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(Created page with "[http://provean.jcvi.org/about.php PROVEAN] was developed to predict whether a protein sequence variation affects protein function. == Module file == The module file can be f...") |
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== Module file == | == Module file == | ||
The module file can be found in this location: | The module file can be found in this location: | ||
/cm/shared/ | /cm/shared/modulefiles/SHARED/ | ||
< | <pre> | ||
#%Module1.0####################################################################### | #%Module1.0####################################################################### | ||
## Provean 1.1.3 modulefile | ## Provean 1.1.3 modulefile | ||
| Line 16: | Line 16: | ||
module-whatis "Adds Provean 1.1.3 to your environment" | module-whatis "Adds Provean 1.1.3 to your environment" | ||
set provean_113_root /cm/shared/apps/ | set provean_113_root /cm/shared/apps/SHARED/provean/provean-1.1.3/bin/ | ||
prepend-path PATH $provean_113_root | prepend-path PATH $provean_113_root | ||
</ | </pre> | ||
== Installation details == | == Installation details == | ||
Compiled from source | Compiled from source. | ||
< | <pre> | ||
./configure --prefix=/cm/shared/apps/ | ./configure --prefix=/cm/shared/apps/SHARED/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/SHARED/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/lustre/shared/public_data_store/nrdb/nrdb_241213/nr | ||
make | make | ||
make install | make install | ||
</ | </pre> | ||
== See also == | == See also == | ||
* [[Globally_installed_software | Globally installed software]] | * [[Globally_installed_software | Globally installed software]] | ||
* [[ABGC_modules | ABGC specific modules]] | * [[ABGC_modules | ABGC specific modules]] | ||
* [[Provean_Sus_scrofa | Mapping all known Sus scrofa variants with Provean]] | |||
== External links == | == External links == | ||
* [http:// | * [http://provean.jcvi.org/downloads/provean.acmbcb.pdf Provean paper] | ||
* [http://provean.jcvi.org/about.php Explanation of Provean algorithm]] | |||
* [http://provean.jcvi.org/downloads/README Provean README] | |||
* [ftp://ftp.ncbi.nih.gov/blast/db/ Location of nr. db. at NCBI] | |||
* [http://weizhong-lab.ucsd.edu/cd-hit/ CD-HIT official website] | |||
Latest revision as of 14:52, 15 June 2023
PROVEAN was developed to predict whether a protein sequence variation affects protein function.
Module file
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/
#%Module1.0#######################################################################
## Provean 1.1.3 modulefile
##
proc ModulesHelp { } {
puts stderr "\tAdds Provean 1.1.3 to your environment"
}
module-whatis "Adds Provean 1.1.3 to your environment"
set provean_113_root /cm/shared/apps/SHARED/provean/provean-1.1.3/bin/
prepend-path PATH $provean_113_root
Installation details
Compiled from source.
./configure --prefix=/cm/shared/apps/SHARED/provean/provean-1.1.3/ PSIBLAST=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/psiblast BLASTDBCMD=/cm/shared/apps/SHARED/blast/ncbi-blast-2.2.28+/bin/blastdbcmd CDHIT=/cm/shared/apps/SHARED/cd-hit/cd-hit-v4.6.1-2012-08-27/cd-hit BLAST_DB=/lustre/shared/public_data_store/nrdb/nrdb_241213/nr make make install
See also
- Globally installed software
- ABGC specific modules
- Mapping all known Sus scrofa variants with Provean