Difference between revisions of "Sequence Alignments"

From Bioinformatikpedia
(New page: == Sequence Alignments == === Sequence searches === * FASTA ../bin/fasta36 sequence.fasta database > FastaOutput.txt * BLAST blastall -p blastp -d database -i sequence.fasta > BlastOutpu...)
 
(→‎Conservation and Gaps)
Line 121: Line 121:
 
|17
  
|17
 
|4,76
  
|4,76
  +
|}
  +
  +
=== Gaps in secondary structure ===
  +
  +
==== ClustalW ====
  +
  +
{| border="1" style="text-align:center; border-spacing:0;"
  +
|'''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 ====
  +
  +
{| border="1" style="text-align:center; border-spacing:0;"
  +
|'''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 ====
  +
  +
{| border="1" style="text-align:center; border-spacing:0;"
  +
|'''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 ====
  +
  +
{| border="1" style="text-align:center; border-spacing:0;"
  +
|'''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 ====
  +
  +
{| border="1" style="text-align:center; border-spacing:0;"
  +
|'''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
 
|}
  
|}
   

Revision as of 23:05, 20 May 2011

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 Avg Gap Length
ClustalW 12 3,75
T-Coffee 25 4,56
T-Coffee (3D) 56 4,75
Cobalt 19 3,26
Muscle 17 4,76

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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