Difference between revisions of "Canavan Task 2 - Sequence alignments"
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===PSIBLAST=== |
===PSIBLAST=== |
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| − | *2 iterations, default Evalue |
+ | *2 iterations, default Evalue 10 |
| − | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2</code> |
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| − | *2 iterations, default Evalue 0.001 |
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| − | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2</code> |
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| − | *10 iterations, default Evalue 0.001 |
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| − | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2</code> |
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| − | *10 iterations, default Evalue 0.001 |
||
**<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2</code> |
**<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2</code> |
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| + | **time: ~2m30 |
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| + | ** 11000 results |
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| + | *2 iterations, E-value cutoff 10E-10 |
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| + | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2 -h</code> |
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| + | *10 iterations, default Evalue 10 |
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| + | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 10</code> |
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| + | *10 iterations, E-value cutoff 10E-10 |
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| + | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 10 -h</code> |
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Revision as of 17:29, 2 May 2012
Sequence
Native ASPA sequence:
UniProt: P45381
>hsa:443 ASPA, ACY2, ASP; aspartoacylase; K01437 aspartoacylase [EC:3.5.1.15] (A)
MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKK
CTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTS
NMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVG
PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA
AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
LTLNAKSIRCCLH
BLASTP
Run BlastP on student machines with big_80 database.
Command:
blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out
-p specifies the blast type
-d database
-i input file
-o output file
We got 195 resulting sequences, out of which the last 101 have EValues below E^-15 and of which none is an Aspartoacylase.
PSIBLAST
- 2 iterations, default Evalue 10
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2- time: ~2m30
- 11000 results
- 2 iterations, E-value cutoff 10E-10
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2 -h
- 10 iterations, default Evalue 10
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 10
- 10 iterations, E-value cutoff 10E-10
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 10 -h
