Difference between revisions of "Sequence Alignments"
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==== T-Coffee 3d ==== |
==== T-Coffee 3d ==== |
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Revision as of 23:17, 20 May 2011
Contents
Sequence Alignments
Sequence searches
- FASTA
../bin/fasta36 sequence.fasta database > FastaOutput.txt
- BLAST
blastall -p blastp -d database -i sequence.fasta > BlastOutput.txt
- PSIBLAST
blastpgp -i sequence.fasta -j iterations -h evalueCutoff -d database > PsiblastOutput.txt
- HHSearch
hhsearch -i query -d database -o output.txt
database = /data/blast/nr/nr
Sequences chosen for the multiple Alignment:
| SeqIdentifier | Seq Identity | source |
|---|---|---|
| 99-90% Sequence Identity | ||
| 56967006|pdb|1X7Z | 99% | PSI BLAST, 3 iterations, E-value cutoff 0.005 |
| 7546384|pdb|1DTW | 95% | BLAST |
| 34810149|pdb|1OLU | 99% | PSI BLAST, 3 iterations, E-value cutoff 10E-6 |
| 13277798|gb|AAH03787.1 | 95% | PSI BLAST, 3 iterations, E-value cutoff 10E-6 |
| 148727347|ref|NP_001092034.1 | 95% | BLAST |
| 89-60% Sequence Identity | ||
| 196011048|ref|XP_002115388.1 | 66% | PSI BLAST, 3 iterations, E-value cutoff 0.005 |
| 149543950|ref|XP_001517857.1 | 67% | BLAST |
| 47227873|emb|CAG09036.1 | 82,5% | FASTA |
| 47196273|emb|CAF88112.1 | 81% | PSI BLAST, 5 iterations, E-value cutoff 0.005 |
| 12964598|dbj|BAB32665.1 | 88% | PSI BLAST, 5 iterations, E-value cutoff 10E-6 |
| 59-40% Sequence Identity | ||
| 193290664|gb|ACF17640.1 | 47% | BLAST |
| 215431443|ref|ZP_03429362.1 | 40% | FASTA |
| 225557347|gb|EEH05633.1 | 51% | PSI BLAST, 3 iterations, E-value cutoff 10E-6 |
| 58267618|ref|XP_570965.1 | 50% | PSI BLAST, 5 iterations, E-value cutoff 0.005 |
| 162449842|ref|YP_001612209.1 | 41% | PSI BLAST, 5 iterations, E-value cutoff 10E-6 |
| 39-20% Sequence Identity | ||
| 56966700|pdb|1W85 | 31% | PSI BLAST, 3 iterations, E-value cutoff 0.005 |
| 5822330|pdb|1QS0 | 38.1% | FASTA |
| 13516864|dbj|BAB40585.1 | 33% | PSI BLAST, 3 iterations, E-value cutoff 10E-6 |
| 284166853|ref|YP_003405132.1 | 35% | PSI BLAST, 5 iterations, E-value cutoff 0.005 |
| 76800932|ref|YP_325940.1 | 34% | PSI BLAST, 5 iterations, E-value cutoff 10E-6 |
Sequences for the Multiple Sequences Alignment were downloaded via NCBI, the sequence id can be changed in the link to retrieve the fasta format: http://www.ncbi.nlm.nih.gov/protein/76800932?report=fasta
Multiple Alignments
clustalw sequences.fasta
t_coffee -seq sequences.fasta
t_coffee -seq sequences.fasta -mode expresso
muscle -in sequences.fasta -out output.aln
download cobalt
./cobalt -i sequences.fasta -norps T > output.aln
Conservation and Gaps
| Alignment methods | Gaps | Conserved Columns | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Gaps | Avg Gap Length | 100% cons | >90% cons | >80% cons | >70% cons | >60% cons | >50% cons | ||
| ClustalW | 12 | 3,75 | 24 | 136 | 53 | 60 | 71 | 91 | |
| T-Coffee | 25 | 4,56 | 24 | 136 | 53 | 60 | 71 | 91 | |
| T-Coffee (3D) | 56 | 4,75 | 21 | 326 | 83 | 92 | 67 | 71 | |
| Cobalt | 19 | 3,26 | 24 | 128 | 68 | 56 | 101 | 72 | |
| Muscle | 17 | 4,76 | 26 | 193 | 26 | 38 | 43 | 10 | |
Gaps in secondary structure
ClustalW
| Gap position | Gap length | Secondary structure |
| 109-110 | 4 | Helix |
| 142-143 | 1 | Helix |
| 235-236 | 1 | Beta strand |
| 276-277 | 11 | Helix |
| 294-295 | 1 | Beta strand |
| 394-395 | 5 | Helix |
T-Coffee
| Gap position | Gap length | Secondary structure |
| 141-142 | 1 | Helix |
| 232-233 | 1 | Beta strand |
| 275-276 | 11 | Helix |
| 310-311 | 1 | Helix |
| 369-370 | 5 | Turn |
| 395-396 | 18 | Helix |
| 398-399 | 5 | Helix |
T-Coffee 3d
| Gap position | Gap length | Secondary structure |
| 101-102 | 1 | Helix |
| 108-109 | 4 | Helix |
| 115-116 | 1 | Helix |
| 116-117 | 1 | Helix |
| 141-142 | 1 | Helix |
| 153-154 | 1 | Beta strand |
| 163-164 | 1 | Helix |
| 177-178 | 3 | Helix |
| 234-235 | 1 | Beta strand |
| 263-264 | 4 | Beta strand |
| 265-266 | 1 | Beta strand |
| 276-277 | 2 | Helix |
| 308-309 | 8 | Helix |
| 309-310 | 5 | Helix |
| 314-315 | 6 | Helix |
| 362-363 | 6 | Helix |
| 371-372 | 4 | Turn |
| 376-377 | 1 | Helix |
| 380-381 | 1 | Helix |
| 382-383 | 7 | Helix |
| 383-384 | 3 | Helix |
| 384-385 | 2 | Helix |
| 387-388 | 2 | Helix |
| 394-395 | 5 | Helix |
Cobalt
| Gap position | Gap length | Secondary structure |
| 108-109 | 4 | Helix |
| 141-142 | 1 | Helix |
| 177-178 | 3 | Helix |
| 276-277 | 11 | Helix |
| 294-295 | 1 | Beta strand |
| 305-306 | 1 | Helix |
| 311-312 | 2 | Helix |
| 387-388 | 1 | Helix |
| 388-389 | 1 | Helix |
| 395-396 | 13 | Helix |
Muscle
| Gap position | Gap length | Secondary structure |
| 109-110 | 4 | Helix |
| 141-142 | 1 | Helix |
| 177-178 | 3 | Helix |
| 276-277 | 11 | Helix |
| 294-295 | 1 | Beta strand |
| 305-306 | 1 | Helix |
| 394-395 | 5 | Helix |
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