Difference between revisions of "Sequence Alignments HEXA"
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We also decided to compare different runs of PsiBlast. We compared PsiBlast with 3 iterations and an e-Value Cutoff of 0.005 and 10E-6 and also two PsiBlast runs with 5 iterations and the same two e-Value cutoffs as before. |
We also decided to compare different runs of PsiBlast. We compared PsiBlast with 3 iterations and an e-Value Cutoff of 0.005 and 10E-6 and also two PsiBlast runs with 5 iterations and the same two e-Value cutoffs as before. |
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− | [[Image:comparison_psiblast|none|300px]] |
+ | [[Image:comparison_psiblast.png|none|300px]] |
Psiblast 1: 3 Iterations, E-Value Cutoff: 0.005 |
Psiblast 1: 3 Iterations, E-Value Cutoff: 0.005 |
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Psiblast 2: 5 Iterations, E-Value Cutoff: 0.005 |
Psiblast 2: 5 Iterations, E-Value Cutoff: 0.005 |
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Psiblast 3: 3 Iterations, E-Value Cutoff: 10E-6 |
Psiblast 3: 3 Iterations, E-Value Cutoff: 10E-6 |
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Psiblast 4: 5 Iterations, E-Value Cutoff, 10E-6 |
Psiblast 4: 5 Iterations, E-Value Cutoff, 10E-6 |
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Revision as of 11:20, 23 May 2011
Sequence Alignments
Sequence Searches:
- FASTA
/bin/fasta36 seq.fasta /data/blast/nr/nr > fasta_out.txt
- BLAST
blastall -p blastp -d /data/blast/nr/nr -i mult_seq.fasta > blast_out.txt
- PSIBLAST
blastpgn -i seq.fasta -j <#iterations> -h <e-value threshold> -d /data/blast/nr/nr > psiblast_out.txt
- HHSearch
For the HHSearch tool we used the online server for HHSearch.
Result Statistics
We wrote a script, which shows the distribution of the E-Value and the Identity and also the different aligned sequences. To analyse the overlap between the different methods, we drew a Venn diagram (with http://bioinfogp.cnb.csic.es/tools/venny/index.html). We compared the BLAST, FASTA and Psiblast method (PsiBlast with 3 and 5 runs and E-Value cutoff from 10E-6)
FASTA found more than 1000 matches, whereas the numbers of results of the blast methods is lower. Therefore, we can see, that FASTA aligns more sequences than blast and therefore, a lot of FASTA hits would be wrong.
We also decided to compare different runs of PsiBlast. We compared PsiBlast with 3 iterations and an e-Value Cutoff of 0.005 and 10E-6 and also two PsiBlast runs with 5 iterations and the same two e-Value cutoffs as before.
Psiblast 1: 3 Iterations, E-Value Cutoff: 0.005
Psiblast 2: 5 Iterations, E-Value Cutoff: 0.005
Psiblast 3: 3 Iterations, E-Value Cutoff: 10E-6
Psiblast 4: 5 Iterations, E-Value Cutoff, 10E-6
The differences between the different PsiBlast variants is not that big. Only Psiblast 1 has 6 aligned sequences, which are not shared by the other variants.
Multiple Alignments
- Cobalt
Download Cobalt from ftp://ftp.ncbi.nlm.nih.gov/pub/cobalt/executables/2.0.1/ (ncbi-cobalt-2.0.1-x64-linux.tar). Uncompress the archive file with tar xfz ncbi-cobalt-2.0.1-x64-linux.tar and change directory to the uncompressed cobalt directoy. Call: ./cobalt -i mult_seq.fasta -norps T > cobalt_out.aln
- ClustalW
clustalw -infile=mult_seq.fasta > clustalW_out.aln
- Muscle
muscle -in mult_seq.fasta -out muscle_out.aln -clw
- T-Coffee
t_coffee -seq mult_seq.fasta
- T-Coffee (3D)
t_coffee -seq mult_seq.fasta -mode expresso