Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments):Results"
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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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− | + | == Comparison == |
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− | + | === Comparing the hits === |
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| [[File:venn_blast_hhblits.png|thumb| Venn diagram of proteins found by BLAST, HHBlits and HHBlits with 8 iterations]] |
| [[File:venn_blast_hhblits.png|thumb| Venn diagram of proteins found by BLAST, HHBlits and HHBlits with 8 iterations]] |
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Venn diagrams created with [http://bioinfogp.cnb.csic.es/tools/venny/index.html Oliveros, J.C. (2007) VENNY. An interactive tool for comparing lists with Venn Diagrams.] |
Venn diagrams created with [http://bioinfogp.cnb.csic.es/tools/venny/index.html Oliveros, J.C. (2007) VENNY. An interactive tool for comparing lists with Venn Diagrams.] |
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− | + | === Comparing the Evalues === |
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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. |
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. |
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+ | == Time == |
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+ | We evaluated the time the programs ran with the command "time" |
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+ | |||
+ | |||
+ | {|style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #000; padding: 0; align: center; " width="85%" |
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+ | ! style="border-style: solid; border-width: 0 1px 1px 0"| Method |
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+ | ! style="border-style: solid; border-width: 0 1px 1px 0"| Parameter |
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+ | ! style="border-style: solid; border-width: 0 1px 1px 0"| Time |
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+ | |- |
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+ | | style="border-style: solid; border-width: 0 1px 1px 0"| Blast v = 700 |
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+ | | style="border-style: solid; border-width: 0 1px 1px 0"| b = 700, v = 700 |
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+ | | style="border-style: solid; border-width: 0 1px 1px 0"| 1m53.944s |
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+ | |- |
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+ | | style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits |
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+ | | style="border-style: solid; border-width: 0 1px 1px 0"| default |
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+ | | style="border-style: solid; border-width: 0 1px 1px 0"| 2m19.519s |
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+ | |- |
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+ | | style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits |
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+ | | style="border-style: solid; border-width: 0 1px 1px 0"| n = 8 |
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+ | | style="border-style: solid; border-width: 0 1px 1px 0"| 16m7.754s |
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+ | |} |
Revision as of 07:42, 5 May 2012
Please see Task 2 for our scripts and line of action on this topic.
Contents
Sequence searches
Blast
Number of hits with Evalue < 0.003: 663
Psi-Blast
HHblits
2 iterations - default
Number of hits with Evalue < 0.003: 326
8 iterations
Number of hits with Evalue < 0.003: 729
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
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 |