Difference between revisions of "Lab journal task 4"
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+ | == Explore structural alignments == |
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+ | |||
The structure assembly was done manually using the results from the sequence search, but also browsing CATH. |
The structure assembly was done manually using the results from the sequence search, but also browsing CATH. |
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We constructed pairwise sequence alignments with Emboss Needle (http://www.ebi.ac.uk/Tools/psa/emboss_needle/) using default parameters to compute the pairwise sequence identity. |
We constructed pairwise sequence alignments with Emboss Needle (http://www.ebi.ac.uk/Tools/psa/emboss_needle/) using default parameters to compute the pairwise sequence identity. |
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== Structural alignments for evaluating sequence alignments == |
== Structural alignments for evaluating sequence alignments == |
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+ | |||
+ | The .hhr input file for hhmakemodel.pl was created with hhsearch using the reference structure 1A6Z_A and the current pdb70 database: |
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+ | hhsearch -i /mnt/home/student/betza/data/1A6Z_A.fasta -d -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70_current_hhm_db -o /mnt/home/student/betza/task4/1A6Z_A_pdb.hhr -Z 10000 -B 10000 |
Revision as of 21:22, 12 August 2013
Explore structural alignments
The structure assembly was done manually using the results from the sequence search, but also browsing CATH. We constructed pairwise sequence alignments with Emboss Needle (http://www.ebi.ac.uk/Tools/psa/emboss_needle/) using default parameters to compute the pairwise sequence identity.
Pymol was used to view the different structures and to construct structural alignments to the template 1A6Z_A. Therfore we used the command " align to structure" from the action menu.
The pymol alignment uses only the C_alpha atoms per default. The following command can be used to align all atoms and create the object ali12
align structure1 and resi 1-n, structure2 and resi 1-m, object=ali12
,where n equals the number of atoms in structure 1 and m the number of atoms in structure 2.
We saved the current view of the first alignment
my_view = cmd.get_view()
and then used this variable later to set the orientation to these values, in order to be able to make images from the different alignments always using the same view.
cmd.set_view(my_view)
<css> table.colBasic2 { margin-left: auto; margin-right: auto; border: 2px solid black; border-collapse:collapse; width: 70%; }
.colBasic2 th,td { padding: 3px; border: 2px solid black; }
.colBasic2 td { text-align:left; }
.colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;} </css>
Apart from Pymol, the following four alignment methods were used from their web interface:
LGA:- superimpose to template structure (second structure, in our case 1A6Z )
- default parameters
- no target structure to specify
- no parameters to set
- score from 0 to 100
- target 1A6Z
- "match"
- default parameters
- target in blue, query in gree
- structurally equivalent residue pairs: orange (query) and red (target)
- S = "structural similarity, if the structurally equivalent parts in query and target match perfectly, S is equal to L. With increasing spatial deviation of the aligned residues, S approaches 0." (https://topmatch.services.came.sbg.ac.at/help/tm_help.html)
- S_r = "Typical distance error" (https://topmatch.services.came.sbg.ac.at/help/tm_help.html)
- no template to specify
- no parameters to set
- jCE algorithm
Structural alignments for evaluating sequence alignments
The .hhr input file for hhmakemodel.pl was created with hhsearch using the reference structure 1A6Z_A and the current pdb70 database:
hhsearch -i /mnt/home/student/betza/data/1A6Z_A.fasta -d -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70_current_hhm_db -o /mnt/home/student/betza/task4/1A6Z_A_pdb.hhr -Z 10000 -B 10000