Difference between revisions of "Canavan Task 2 - Sequence alignments"
| Line 34: | Line 34: | ||
===PSIBLAST=== |
===PSIBLAST=== |
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| − | *2 iterations, default Evalue |
+ | *2 iterations, default Evalue 0.002 |
| − | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o |
+ | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it2_p45381_wt_big80.out -j 2</code> |
**time: ~2m30 |
**time: ~2m30 |
||
** 197 results |
** 197 results |
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| Line 46: | Line 46: | ||
**<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2 -h 10e-10</code> |
**<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2 -h 10e-10</code> |
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| + | *5 iterations, default Evalue 0.002 |
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| + | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it5_p45381_wt_big80.out -j 2</code> |
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| + | |||
| + | |||
| + | |||
| + | *10 iterations, default Evalue 0.002 |
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| + | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it10_p45381_wt_big80.out -j 10</code> |
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| + | **time: ~10m |
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| + | **stopped after 8 rounds |
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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 |
*10 iterations, E-value cutoff 10E-10 |
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Revision as of 18:09, 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. Most of the resulting proteins are Aspartoacylases of other species. Most of the results with EValue > E^-15 are Succinylglutamate Desuccinylases, which catalyze a reaction similar to Aspartoacylase.
PSIBLAST
- 2 iterations, default Evalue 0.002
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it2_p45381_wt_big80.out -j 2- time: ~2m30
- 197 results
- best E-Value: E^-164
- 93 results with EValue < e^-15 of which most are (probable or putative)Aspartoacylases
- proteins > EValue e^-15 are often Succinylglutamate Desuccinylases
- results similar to blastp run
- 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 10e-10
- 5 iterations, default Evalue 0.002
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it5_p45381_wt_big80.out -j 2
- 10 iterations, default Evalue 0.002
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it10_p45381_wt_big80.out -j 10- time: ~10m
- stopped after 8 rounds
- 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 10e-10
