Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments):Results"
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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 |
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== 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]]) |
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=== 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). |
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==== 2 iterations - default ==== |
==== 2 iterations - default ==== |
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{| 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 == |
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=== Comparing the hits === |
=== Comparing the hits === |
Revision as of 08:45, 5 May 2012
Please see Task 2 for our scripts and line of action on this topic.
Contents
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
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
Number of hits with Evalue < 0.003: 326
8 iterations
Number of hits with Evalue < 0.003: 729
The first HHblits run took about 2.5 minutes, the second one about 16 minutes (see section Time).
Comparison
Comparing the hits
Venn diagrams created with Oliveros, J.C. (2007) VENNY. An interactive tool for comparing lists with Venn Diagrams.
Comparing the Evalues
![Fabry animation.gif](/wiki/images/0/08/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 |
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Blast v = 700 | b = 700, v = 700 | 1m53.944s |
HHBlits | default | 2m19.519s |
HHBlits | n = 8 | 16m7.754s |