Running a PSIBLAST search with two different databanks - one to create the PSSM, the other to get sequences:
blastpgp -d nr -i subI -j 5 -C subI.ckp -a 2 -o subI.out -h 0.00001 -F f
blastpgp -d swissprot -i gamma -j 5 -C gamma.ckp -a 2 -o gamma.out -h 0.00001 -F f
Runs a 4 iterations of a PSIblast
the -h option tells the program to use matches with
E <10^-5 for the next iteration,
-C
creates a checkpoint (called subI.ckp),
-o writes the output to subI.out,
-i option specifies input as
using subI as input (a fasta formated aa sequence).
The nr databank used is stored in /common/data/
-a 2 use two processors
(It might help to use the node wih more memory (017)-not!)
blastpgp -d /Users/jpgogarten/genomes/msb8.faa -i subI -a 2 -R subI.ckp -o subI.out3 -F f
blastpgp -d /Users/jpgogarten/genomes/msb8.faa -i gamma -a 2 -R gamma.ckp -o gamma.out3 -F f
Runs another iteration of the same blast search, but uses the databank /Users/jpgogarten/genomes/msb8.faa
-R tells the program where to resume
-d specifies a different databank
-i input file - same sequence as before
-o outputfile
-a 2 use two processors
(example in blasttemp3)
Phylogenetic reconstruction:
This is how far we got -- more in class 10