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