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

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(Comparing the Evalues)
 
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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.
 
 
== Sequence searches ==
 
=== Blast ===
 
{| class="centered"
 
| [[File:Blastsearch_default_v700_ids_GOterms_comparison.png|thumb| 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]]
 
| [[File:blastsearch_default_v700_Evalues.png|thumb| Histogram of the logarithmic E-values of the BLAST hits for P06280]]
 
|}
 
{| class="centered"
 
| [[File:blastsearch_default_v700_Positives.png|thumb| Histogram of the positive amino acids of the pairwise alignments of the BLAST hits for P06280]]
 
| [[File:blastsearch_default_v700_Identities.png|thumb| Histogram of the identical amino acids of the pairwise alignments of the BLAST hits for P06280]]
 
| [[File:blastsearch_default_v700_Lengths.png|thumb| Histogram of the length of the BLAST hits for P06280]]
 
|}
 
 
Number of hits with Evalue < 0.003: 663
 
 
=== Psi-Blast ===
 
 
 
=== HHblits ===
 
==== 2 iterations - default ====
 
{| class="centered"
 
| [[File:hhblits_default_ids_GOterms_comparison.png|thumb| 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]]
 
| [[File:hhblits_default.out_Evalues.png|thumb| Histogram of the logarithmic E-values of the HHblits hits for P06280]]
 
|}
 
 
Number of hits with Evalue < 0.003: 326
 
{| class="centered"
 
| [[File:hhblits_default_Similarity.png|thumb| Histogram of the similarity of the HHblits hits to P06280]]
 
| [[File:hhblits_default_Identities.png|thumb| Histogram of the identical amino acids of the pairwise alignments of the HHblits hits for P06280]]
 
|}
 
 
==== 8 iterations ====
 
{| class="centered"
 
| [[File:hhblits_n8_neu_ids_GOterms_comparison.png|thumb| 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]]
 
| [[File:hhblits_n8_neu.out_Evalues.png|thumb| Histogram of the logarithmic E-values of the HHblits search with 8 iterations for P06280]]
 
|}
 
 
Number of hits with Evalue < 0.003: 729
 
{| class="centered"
 
| [[File:hhblits_n8_neu_Similarity.png|thumb| Histogram of the similarity of the BLAST hits (search with 8 iterations) to 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]]
 
|}
 
=== Comparison ===
 
==== Comparing the hits ====
 
{| class="centered"
 
| [[File:venn_blast_hhblits.png|thumb| Venn diagram of proteins found by BLAST, HHBlits and HHBlits with 8 iterations]]
 
| [[File:venn_blast_psi_hhblits.png|thumb| Venn diagram of the proteins found by BLAST, Psi-BLAST (10 iterations and E-value cutoff 10e-10 ) and HHBlits with 8 iterations]]
 
| [[File:venn_blast_hhblits_best100.png|thumb| Venn diagram of the first 100 proteins found by BLAST, HHBlits and HHBlits with 8 iterations]]
 
| [[File:venn_blast_psi_hhblits_best100.png|thumb| Venn diagram of the first 100 proteins found by BLAST, Psi-BLAST and HHBlits with 8 iterations]]
 
|}
 
 
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.]
 
 
==== Comparing the Evalues ====
 
[[File:Fabry_animation.gif]] On the left hand side you can see a histogram of the distribution of the E-values, when the search is performed with different methods.
 
The R Script is based on Andrea's [[ARSA_search_protocol 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.
 

Latest revision as of 21:00, 6 May 2012