Difference between revisions of "Sequence searches and multiple sequence alignments (Phenylketonuria)"
From Bioinformatikpedia
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(→PSI-BLAST (Position-Specific Iterated BLAST)) |
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=== PSI-BLAST (Position-Specific Iterated BLAST) === |
=== PSI-BLAST (Position-Specific Iterated BLAST) === |
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| − | For PSI-Blast ([http://www.ncbi.nlm.nih.gov/books/NBK2590/ 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. |
+ | For PSI-Blast ([http://www.ncbi.nlm.nih.gov/books/NBK2590/ 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 |
blastpgp -i /mnt/home/student/worfk/Masterpractical/Task2/PAH.fasta -d /mnt/project/rost_db |
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Revision as of 17:25, 4 May 2013
Contents
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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