Difference between revisions of "Canavan Task 2 - Sequence alignments"

From Bioinformatikpedia
(PSIBLAST)
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**<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>
 
** time: ~2m30
 
** time: ~2m30
** 197 results
+
** 500 results
 
** best E-Value: E^-142
 
** best E-Value: E^-142
** worst E-Value:
+
** worst E-Value: 3E^-4
** 93 results with EValue < e^-15 of which most are (probable or putative) Aspartoacylases
+
** Results with best EValues are mostly Aspartoacylases
  +
** New results from 2nd iteration are mostly Succi..
** proteins > EValue e^-15 are often Succinylglutamate Desuccinylases
 
  +
** results similar to blastp run
 
   
 
*2 iterations, E-value cutoff 10E-10
 
*2 iterations, E-value cutoff 10E-10

Revision as of 18:39, 2 May 2012

Task 2 : Canavans Disease

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

Run PsiBlast on student machines with big_80 database.

  • 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
    • 500 results
    • best E-Value: E^-142
    • worst E-Value: 3E^-4
    • Results with best EValues are mostly Aspartoacylases
    • New results from 2nd iteration are mostly Succi..


  • 2 iterations, E-value cutoff 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

HHBLITS

Run HHBlits on student machines with Uniprot20 database.

hhblits -i P45381_wt.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_default.out -E 0.003 -Ofas hhblits_msa_default.txt -n 8