Difference between revisions of "Canavan Task 2 - Sequence alignments"
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=== Sequence === |
=== Sequence === |
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| − | + | The native ASPA sequence that we used for the current task is shown below: |
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UniProt: P45381 |
UniProt: P45381 |
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=== BLASTP === |
=== BLASTP === |
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| − | + | First, we ran BlastP on student machines with the big_80 as a reference database. |
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Command: |
Command: |
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<code>blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out</code> |
<code>blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out</code> |
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| − | |||
| − | -p specifies the blast type<br> |
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| − | -d database<br> |
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| − | -i input file<br> |
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| − | -o output file<br> |
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We got 195 resulting sequences, out of which the last 101 have EValues below E^-15. |
We got 195 resulting sequences, out of which the last 101 have EValues below E^-15. |
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===PSIBLAST=== |
===PSIBLAST=== |
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| − | + | PSIBlast was used in the same fashion as BLAST, with the big_80 as the background database. Results: |
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| − | *2 iterations |
+ | * Running 2 iterations and default E-Value 0.002 |
**<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it2_p45381_wt_big80.out -j 2</code> |
**<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it2_p45381_wt_big80.out -j 2</code> |
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** time: ~2m30 |
** time: ~2m30 |
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** worst E-Value: 3E^-4 |
** worst E-Value: 3E^-4 |
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** Results with best EValues are mostly Aspartoacylases |
** Results with best EValues are mostly Aspartoacylases |
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| − | ** Sequences previously not found are mostly |
+ | ** Sequences previously not found are mostly Succinylglutamate Desuccinylases |
| − | *2 iterations, E-value cutoff 10E-10 |
+ | *2 iterations, more strict E-value cutoff of 10E-10 |
**<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it2_h10e10_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 psiblast_it2_h10e10_p45381_wt_big80.out -j 2 -h 10e-10</code> |
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** time ~2m30 |
** time ~2m30 |
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Revision as of 16:40, 6 May 2012
Sequence
The native ASPA sequence that we used for the current task is shown below:
UniProt: P45381
>hsa:443 ASPA, ACY2, ASP; aspartoacylase; K01437 aspartoacylase [EC:3.5.1.15] (A)
MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKK
CTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTS
NMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVG
PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA
AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
LTLNAKSIRCCLH
BLASTP
First, we ran BlastP on student machines with the big_80 as a reference database.
Command:
blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out
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
PSIBlast was used in the same fashion as BLAST, with the big_80 as the background database. Results:
- Running 2 iterations and default E-Value 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
- 500 results
- best E-Value: E^-142
- worst E-Value: 3E^-4
- Results with best EValues are mostly Aspartoacylases
- Sequences previously not found are mostly Succinylglutamate Desuccinylases
- 2 iterations, more strict E-value cutoff of 10E-10
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it2_h10e10_p45381_wt_big80.out -j 2 -h 10e-10- time ~2m30
- 93 results
- best E Value: E^-145
- worst E Value: 2E-29
- results mainly Aspartoacylases
- 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
- converged after 8 rounds
- 500 results
- best E-Value 5E^-70
- worst E-Value 8E^-38
- most significant results include more Succinylglutamate Desuccinylases than Aspartoacylases
- 10 iterations, E-value cutoff 10E-10
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it10_h10e10_p45381_wt_big80.out -j 10 -h 10e-10- time: ~10m
- all 10 iterations were done (no early convergence)
- 500 results
- best E-Value: 7E^-70
- worst E-Value: 1E^-38
- aspartoacylases slightly more frequent in lower E-Values (< E-58), but no significant difference in E-Values for aspas and succis
HHBLITS
Run HHBlits on student machines with Uniprot20 database.
hhblits -i P45381_wt.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -o hhblits_p45381_def.out- time: 2m50
- 274 results
- best E-Value: 2E^-110
- worst E-Value: 0.0011
- mixed results with Aspa and Succi
hhblits -i P45381_wt.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -o hhblits_p45381_n10.out
-n number of iterations (def 2)
-e E Value CutOff (0.001)
