Difference between revisions of "Sequence and multiple alignments"
(→Sequence Alignments) |
(→Database search) |
||
| Line 4: | Line 4: | ||
We used different tools for the search in a non-reduntant(NR) database like BLAST, FASTA and PSI-BLAST. Because of the absence of the database in a hmm format, we decided not to integrate the hhpred web-results. These results are not compareable. |
We used different tools for the search in a non-reduntant(NR) database like BLAST, FASTA and PSI-BLAST. Because of the absence of the database in a hmm format, we decided not to integrate the hhpred web-results. These results are not compareable. |
||
| + | We called BLAST and FASTA with the standart parameter. |
||
| − | Blastaufruf: ''blast -p blastp -i 1a6z.fasta -d /data/nr/nr -o blastp_1a6z_on_NR.txt'' runtime 5:34<br> |
||
| − | + | ''blast -p blastp -i 1a6z.fasta -d /data/nr/nr -o blastp_1a6z_on_NR.txt'' runtime 5:34<br> |
|
| + | ''../../Desktop/fasta-36.3.4/bin/fasta36 -q 1a6z.fasta /data/nr/nr >fasta_1a5z_on_nr.txt'' the runtime was 10:44.<br> |
||
<br> |
<br> |
||
| + | PSI-BLAST was used with different parameter settings. |
||
| − | psiblast: ''blastpgp -i 1a6z.fasta -d /data/nr/nr'' runtime 21:40 <br> |
||
| + | ''blastpgp -i 1a6z.fasta -d /data/nr/nr'' runtime 21:40 <br> |
||
''blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 -e 10E-6 > psiblast_on_NR_itera3_e-val_10E-6.txt'' runtime 23:49<br> |
''blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 -e 10E-6 > psiblast_on_NR_itera3_e-val_10E-6.txt'' runtime 23:49<br> |
||
''blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 -e 10E-6 > psiblast_on_NR_itera6_e-val_10E-6.txt'' runtime 15:08<br> |
''blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 -e 10E-6 > psiblast_on_NR_itera6_e-val_10E-6.txt'' runtime 15:08<br> |
||
''blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 > psiblast_on_NR_itera3.txt'' runtime 9:41<br> |
''blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 > psiblast_on_NR_itera3.txt'' runtime 9:41<br> |
||
| − | ''blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 > psiblast_on_NR_itera6.txt'' runtime 23:30 |
+ | ''blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 > psiblast_on_NR_itera6.txt'' runtime 23:30<br> |
| + | We also compared the runtime of the different tools. For PSI-BLAST, in our case, the e-Value and the number of iterations had no impact on the results. |
||
[[File:Overlap.png|thumb|]] |
[[File:Overlap.png|thumb|]] |
||
Revision as of 18:35, 23 May 2011
Sequence Alignments
Database search
We used different tools for the search in a non-reduntant(NR) database like BLAST, FASTA and PSI-BLAST. Because of the absence of the database in a hmm format, we decided not to integrate the hhpred web-results. These results are not compareable.
We called BLAST and FASTA with the standart parameter.
blast -p blastp -i 1a6z.fasta -d /data/nr/nr -o blastp_1a6z_on_NR.txt runtime 5:34
../../Desktop/fasta-36.3.4/bin/fasta36 -q 1a6z.fasta /data/nr/nr >fasta_1a5z_on_nr.txt the runtime was 10:44.
PSI-BLAST was used with different parameter settings.
blastpgp -i 1a6z.fasta -d /data/nr/nr runtime 21:40
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 -e 10E-6 > psiblast_on_NR_itera3_e-val_10E-6.txt runtime 23:49
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 -e 10E-6 > psiblast_on_NR_itera6_e-val_10E-6.txt runtime 15:08
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 > psiblast_on_NR_itera3.txt runtime 9:41
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 > psiblast_on_NR_itera6.txt runtime 23:30
We also compared the runtime of the different tools. For PSI-BLAST, in our case, the e-Value and the number of iterations had no impact on the results.
Multiple Alignments
Multiple Alignments
Used Sequences
| SeqIdentifier | Seq Identity | source | Protein function |
|---|---|---|---|
| 99-90% Sequence Identity | |||
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| 89-60% Sequence Identity | |||
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| 59-40% Sequence Identity | |||
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| 39-20% Sequence Identity | |||
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
| xxx | % | xxx | xxx |
The sequences with <20% and >99% sequence identitiy were ignored and 5 samples were randomly picked from the other ranges. So 20 sequences were available for the multiple alignments. Unfortunately no sequences in the range between 99-90% with known 3D-structure were found, so only sequences without known structure were used here.
