Running BLAST in SRS6

José R. Valverde jr at cnb.uam.es
Fri Feb 18 04:26:57 EST 2000


I've been having trouble to run Blast on SRS6 using the icarus files out
of the box. Having had a look at it I see running FASTA would have been
problematic too. In the end I made a number of changes in various files
to make it run:

	On "srsdb.i" there is a $BdbRoot variable wich supposedly points
to the database directory. So far so good. HOWEVER, it is NOT used at all
which is misleading.

	First, on all blast?.i files the "setenv BLASTDB" line is commented
and does not point to the database directory as it should.

	Second, BLAST uses for the search set a variable from "fasta.i"
which instead of using "BdbRoot" hardcodes the database location arbitraily
as $dataRoot/blast/whatever WHICH completely ignores the variable AND
further imposes an arbitrary directory name for the databases.

	What I'm doing is
	
	- uncommenting the setenv BLASTDB variables in all blast?.i files
script definition section (at the bottom of the file)

	- adding a new variable to "srsdb.i", just by $BdbRoot to independize
FASTA and BLAST (just in case):

	$FdbRoot = "/data/gen/fastadb/"
	$BdbRoot 0 "/data/gen/blastdb/"

	- modifying "fasta.i" to use the appropriate variable for FASTA
instead of the hardcoded value:

# protein databases available for all fasta programs
$FastaProtDB_Option=$AppOpt:[search  guiType:menu pos:next group:$PRIM_OPTS
      prompt:'Database to search:' values:{
        $OptVal:['SWISSNEW' valStr:'$FdbRoot/swissnew' on:y]
#                                   ^^^^^^^^ XXX JR XXX
        $OptVal:['SWISSPROT' valStr:'$FdbRoot/swissprot']
#                                    ^^^^^^^^ XXX JR XXX
       }
    ]
# DNA databases available for all fasta programs
$FastaDnaDB_Option=$AppOpt:[search  guiType:menu pos:next group:$PRIM_OPTS
      prompt:'Database to search:' values:{
        $OptVal:['EMBLNEW' valStr:'$FdbRoot/emblnew']
#                                  ^^^^^^^^ XXX JR XXX
       }
    ]

Up to here it should work is you have BLAST and FASTA databases in the same
directory. 

	- Just in case you don't, which I prefer to manage in "srsdb.i "
directory variable definitions, I'm modifying the "fasta.i" file to
define the database search set options as follows (just before the 
$Fasta*DB_Option definitions). I'm doing it on fasta.i 'cos doing it in
blast.i didn't work and I don't have enough time:

# XXX - JR - XXX
# protein databases available for all blast programs
$BlastProtDB_Option=$AppOpt:[search  guiType:menu pos:next group:$PRIM_OPTS
      prompt:'Database to search:' values:{
        $OptVal:['SWISSNEW' valStr:'$BdbRoot/swissnew' on:y]
        $OptVal:['SWISSPROT' valStr:'$BdbRoot/swissprot']
       }
    ]
# DNA databases available for all blast programs
$BlastDnaDB_Option=$AppOpt:[search  guiType:menu pos:next group:$PRIM_OPTS
      prompt:'Database to search:' values:{
        $OptVal:['EMBLNEW' valStr:'$BdbRoot/emblnew']
       }
    ]
# XXX - JR - XXX


	- and then modifying all "blast?.i" files to use Blast*DB_Option
instead of Fasta*DB_Option in the Application definition, e.g. on "blastp.i"

$BLASTP_APP=$Application:[BlastP
  title:'Sequence Similarity Search' resultDb:$BLASTP_DB
  options:{
    $jobName_Option
    # $FastaProtDB_Option is defined in fasta.i - can be used if fasta and blast 
    # databases in same directory
#XXX - JR - XXX    $FastaProtDB_Option
    $BlastProtDB_Option
    $ProtSeqInput_Option
...


This way it works, and allows for finer control of FASTA and BLAST database
location simply  tweaking srsdb.i.

				j


-- 
	These opinions are mine and only mine. Hey man, I saw them first!

			    Jose R. Valverde
				EMBnet/CNB

	De nada sirve la Inteligencia Artificial cuando falta la Natural
There is no sense in Artificial Intelligence in the absence of Natural Intelligence





More information about the Bio-srs mailing list