Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments):Results"

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(→‎Sequence searches)
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Please see [[Fabry:Sequence_alignments_(sequence_searches_and_multiple_alignments) | Task 2 ]] for our scripts and line of action on this topic.
  
Please see [[Fabry:Sequence_alignments_(sequence_searches_and_multiple_alignments) | Task 2 ]] for our scripts and line of action on this topic.
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== Reference sequence ==
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The reference sequence of [[Alpha-galactosidase|α-Galactosidase A]] that will be used in this task was obtained from Swissprot [http://www.uniprot.org/uniprot/P06280 P06280].
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>gi|4504009|ref|NP_000160.1| alpha-galactosidase A precursor [Homo sapiens]
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MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFM
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EMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNK
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TCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWP
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FQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQ
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VTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWA
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VAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENT
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MQMSLKDLL
   
 
== Sequence searches ==
  
== Sequence searches ==
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Number of hits with Evalue < 0.003: 663
  
Number of hits with Evalue < 0.003: 663
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The run took about 2 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]])
   
 
=== Psi-Blast ===
  
=== Psi-Blast ===
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=== HHblits ===
  
=== HHblits ===
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We searched the "big80" database with HHblits using the default settings and also with the maximum number of possible iterations (8).
 
==== 2 iterations - default ====
  
==== 2 iterations - default ====
 
{| class="centered"
  
{| class="centered"
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| [[File:hhblits_n8_neu_Identities.png|thumb| Histogram of the identical amino acids of the pairwise alignments of the BLAST hits (search with 8 iterations) for P06280]]
  
| [[File:hhblits_n8_neu_Identities.png|thumb| Histogram of the identical amino acids of the pairwise alignments of the BLAST hits (search with 8 iterations) for P06280]]
 
|}
  
|}
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The first HHblits run took about 2.5 minutes, the second one about 16 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]]).
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== Comparison ==
  
== Comparison ==
 
=== Comparing the hits ===
  
=== Comparing the hits ===

Revision as of 07:45, 5 May 2012

Please see Task 2 for our scripts and line of action on this topic.

Reference sequence

The reference sequence of α-Galactosidase A that will be used in this task was obtained from Swissprot P06280. 

>gi|4504009|ref|NP_000160.1| alpha-galactosidase A precursor [Homo sapiens]
MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFM
EMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNK
TCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWP
FQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQ
VTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWA
VAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENT
MQMSLKDLL

Sequence searches

Blast

GO terms of P06280 and each BLAST hit (with Evalue <= 0.003) compared. Percentage terms shared, in relation to number of GO terms of P06280 (AGAL_HUMAN) in the upper picture, in the secon picture in relation to number of each hit
Histogram of the logarithmic E-values of the BLAST hits for P06280
Histogram of the positive amino acids of the pairwise alignments of the BLAST hits for P06280
Histogram of the identical amino acids of the pairwise alignments of the BLAST hits for P06280
Histogram of the length of the BLAST hits for P06280

Number of hits with Evalue < 0.003: 663


The run took about 2 minutes (see section Time)

Psi-Blast

HHblits

We searched the "big80" database with HHblits using the default settings and also with the maximum number of possible iterations (8).

2 iterations - default

GO terms of P06280 and each HHblits hit (with Evalue < 0.003) compared. Percentage terms shared, in relation to number of GO terms of P06280 (AGAL_HUMAN) in the upper picture, in the secon picture in relation to number of each hit
Histogram of the logarithmic E-values of the HHblits hits for P06280

Number of hits with Evalue < 0.003: 326

Histogram of the similarity of the HHblits hits to P06280
Histogram of the identical amino acids of the pairwise alignments of the HHblits hits for P06280

8 iterations

GO terms of P06280 and each HHblits hit (with Evalue < 0.003 and 8 iterations) compared. Percentage terms shared, in relation to number of GO terms of P06280 (AGAL_HUMAN) in the upper picture, in the secon picture in relation to number of each hit
Histogram of the logarithmic E-values of the HHblits search with 8 iterations for P06280

Number of hits with Evalue < 0.003: 729

Histogram of the similarity of the BLAST hits (search with 8 iterations) to P06280
Histogram of the identical amino acids of the pairwise alignments of the BLAST hits (search with 8 iterations) for P06280


The first HHblits run took about 2.5 minutes, the second one about 16 minutes (see section Time).

Comparison

Comparing the hits

Venn diagram of proteins found by BLAST, HHBlits and HHBlits with 8 iterations
Venn diagram of the proteins found by BLAST, Psi-BLAST (10 iterations and E-value cutoff 10e-10 ) and HHBlits with 8 iterations
Venn diagram of the first 100 proteins found by BLAST, HHBlits and HHBlits with 8 iterations
Venn diagram of the first 100 proteins found by BLAST, Psi-BLAST and HHBlits with 8 iterations

Venn diagrams created with Oliveros, J.C. (2007) VENNY. An interactive tool for comparing lists with Venn Diagrams.

Comparing the Evalues

Fabry animation.gif

Above you can see a histogram of the distribution of the E-values, for the search performed with different methods. The R Script is based on Andrea's R Script psiBlast.evalueHist.Rscript

As one can clearly see, the number of significant hits in the Psi-Blast search exceeds the number of hits in any of the other two searches by far. Also this histogram looks more like a normal distribution with mean -80, while the histograms of the BLAST and the HHBlits search do not, but rather tend towards the zero point. The least hits are generated by the "ordinary" BLAST search (663), the Psi-BLAST search finds the ten-fold number (6868). Thus in respect to the E-values I would prefer using Psi-Blast.

Time

We evaluated the time the programs ran with the command "time"


Method Parameter Time
Blast v = 700 b = 700, v = 700 1m53.944s
HHBlits default 2m19.519s
HHBlits n = 8 16m7.754s
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