Difference between revisions of "ARS A Sequence alignments"

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=== Blast ===
 
=== Blast ===
   
[[File:ARSA_blastHistogram_id.png|thumb|200px|BLAST result: distribution of percent sequence identity of unique matches]] [[File:ARSA_blastHistogram_eVal.png|thumb|200px|BLAST result: distribution of eValues of unique matches]]
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[[File:ARSA_blastHistogram_id.png|thumb|200px|BLAST result: distribution of percent sequence identity of unique matches]] [[File:ARSA_blastHistogram_eVal.png|thumb|200px|BLAST result: distribution of e-values of unique matches]]
   
 
* This simple search finds 3763 sequence matches with an e-value better (smaller) than the default 10.
 
* This simple search finds 3763 sequence matches with an e-value better (smaller) than the default 10.

Revision as of 12:51, 30 April 2012

In this task, we explore the sequence space around the Human lysosomal arylsulfatase A (ARS A).

Sequence searches

We compare different methods to search a database of non-redundant proteins (for details see protocol).

Blast

BLAST result: distribution of percent sequence identity of unique matches
BLAST result: distribution of e-values of unique matches
  • This simple search finds 3763 sequence matches with an e-value better (smaller) than the default 10.
  • Of these, 3120 have an e-value matching the default criterion for inclusion in the iterative BLAST.
  • Some of the sequence matches occur twice with different alignments. The number of unique sequence matches is: 3513.
  • The distributions of percent sequence identity and e-Values shows that there are many sequence matches between 20 and 40 percent sequence identity and that the majority of e-Values is around 10^-6.
  • The blast search in big_80 finds only one matching pdb entry. However, this is partly due to the way of clustering used for big_80 (based on CD_hit), where long sequences are preferred over shorter ones.

PSI-Blast

Runtimes depending on parameters
Runtime [s] j = 2 j = 10
h = 0.002 280 2111
h = 10E-10 280 2040
  • Running iterative blasts takes a while (see table "Runtimes depending on parameters"). The more iterations, the longer the run-time. However, decreasing the inclusion threshold speeds up the process since fewer sequences are added to the profile.
Number of unique matches depending on parameters
# unique matches j = 2 j = 10
h = 0.002 6421 7554
h = 10E-10 7115 8366
  • The number of unique matches increases with more iterations (see table "Number of unique matches depending on parameters"). Notably, the number of unique matches increases with decreased inclusion threshold. Probably the PSSM built with stricter inclusion is more specific and therefore produces more significant hits.
  • The
    PSI-BLAST result: distribution of e-values of unique matches
    distribution of e-values shifts to higher (less meaningful) e-values with more iterations and to lower (more meaningful) e-values with more stringent inclusion cutoff.

Comparison

Multiple sequence alignments