Please see Task 2 for our scripts and line of action on this topic.
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
Psi-Blast
HHblits
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 |
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
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.
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
