Tastk 2: Alignments

Sequence Searches

TODO: what blast parameters should be used?

Blast:
blastall -i /mnt/home/student/betza/data/hfe.fasta -d /mnt/project/pracstrucfunc13/data/big/big_80 -O /mnt/home/student/betza/task2/hfe_blast.txt -p blastp

HHblits parameter:
hhblits -i /mnt/home/student/betza/data/hfe.fasta -d /mnt/project/rost_db/data/hhblits/uniprot20_02Sep11 -o /mnt/home/student/betza/task2/hfe.hhr -oa3m /mnt/home/student/betza/task2/hfe.a3m -oalis /mnt/home/student/betza/task2/hfe -ohhm /mnt/home/student/betza/task2/hfe.hhm