Sequence searches and multiple sequence alignments (Phenylketonuria)

Summary of the task

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Sequence searches

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

BLAST (Basic Local Alignment Search Tool)

nohup 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 1000 -b 1000 -o psi_blast_big_80_2_2.out -C big_80_check_
2_2.chk -Q big_80_matrix_2_2.pssm

HHblits

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To perform all programms at once, one could use the Perl-script from Maria, like shown here:

perl /mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1/run.pl ...

Comparison of the results

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Multiple sequence alignments

ClustalW

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Muscle

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T-Coffee

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