Difference between revisions of "Sequence Alignments HEXA"
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− | 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. |
+ | 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. The two different Psi-Blast variants showed a big agreement by their aligned sequences, and all their sequences were also aligned by FASTA. All sequences, which were aligned by Blast were also found by the FASTA alignment. |
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. |
Revision as of 11:22, 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. The two different Psi-Blast variants showed a big agreement by their aligned sequences, and all their sequences were also aligned by FASTA. All sequences, which were aligned by Blast were also found by the FASTA alignment.
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