New BLAST+ PCD Menus
From Bioinformatics.Org Wiki
Assigned to: Drexler Hernandez
The goal is to update the blmenus for the new BLAST+2.2.26 programs from NCBI, that replace the old blastcl3 client.
||compares protein query to protein database
||blprotein --> Database --> blastp
||compares an auto-translated DNA query to a protein database
||bldna --> Database --> blastx
||compares a DNA query to a DNA database
||bldna --> Database --> blastn
||compares a protein query to an auto-translated DNA database
||blprotein --> Database --> tblastn
||compares an auto-translated DNA query to an auto-translated DNA database
||bldna --> Database --> tblastx
|* auto-translation of DNA to protein -
Programs like BLAST and FASTA can translate DNA to protein on the fly.
This is a very crude translation, involving nothing more than taking
every three nucleotides and substituting in the corresponding amino
acid. Thus, no information is used regarding introns or transcription
initiation or termination sites. Consequently, even non-coding DNA will
get translated into protein!
A new blastp blmenu has already been created. Your job is to create blmenus for the remaining four blast programs, in the order shown above.
Getting up to speed
- Tutorial: Use BLASTP to search for sequences related to a query protein, within a specific taxonomic group
- TUTORIAL: CREATING DATASETS OF RELATED SEQUENCES
- NCBI BLAST web site - shows how to run BLAST on the web http://blast.ncbi.nlm.nih.gov/Blast.cgi
- NCBI documentationn for BLAST on the BIRCH web site
Getting things in place
Update your current BIRCH to the current Development Version
Update your copy of BIRCH with both the framework and binaries from the current Development version using the update procedure found in the BIRCH Administrator's Guide
For each program
- create a copy of the blmenu file in $BIRCH/local
- modify the PCD of the blmenu file using guidance from
- the new blastp menu
- the NCBI web blast page
- the manual page for that program
Get blastx working and contact Brian when it's ready. We'll go over the menu and I will make suggestions regarding how to do the remaining programs.