Lab Journal - Task 2 (PAH)

Sequence searches

The following invocations were used for Blast, PSI-Blast and HHBlits:

BLAST (Basic Local Alignment Search Tool)

blastall -p blastp -d /mnt/project/rost_db/data/big/big_80 -i /mnt/home/student/worfk
/Masterpractical/Task2/PAH.fasta -o /mnt/home/student/worfk/Masterpractical/Task2/Blast/PAH
_Blast_big_80.out -v 2000 -b 2000

PSI-BLAST (Position-Specific Iterated BLAST)

For PSI-Blast (PSI-BLAST Tutorial) more than one vocation was performed. First two iterations were done with an E-value cutoff of 0.002 and then again with cutoff 10E-10. The same for ten iterations. An example vocation would be:

blastpgp -i /mnt/home/student/worfk/Masterpractical/Task2/PAH.fasta -d /mnt/project/rost_db
/data/big/big_80 -j 2 -h 0.002 -v 2000 -b 2000 -o psi_blast_big_80_2_2.out -C big_80_check_
2_2.chk -Q big_80_matrix_2_2.pssm

HHblits

hhblits -i /mnt/home/student/waldraffs/Masterpraktikum/PAH.fasta -d /mnt/project/rost_db/data/hhblits/uniprot20_02Sep11 
-o /mnt/home/student/waldraffs/Masterpraktikum/PAH_2000.hrr -oa3m /mnt/home/student/waldraffs/Masterpraktikum/PAH_2000.a3m 
-ohhm /mnt/home/student/waldraffs/Masterpraktikum/PAH_2000.hhm -Z 2000 -B 2000

Multiple sequence alignments

ClustalW

clustalw -align -infile=in.fasta -outfile=out.aln

Muscle

muscle -in in.fasta -clw -out out.aln

T-Coffee

t_coffee in.fasta