Difference between revisions of "Lab Journal of Task 4 (MSUD)"
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== Use structural alignments to evaluate sequence alignments == |
== Use structural alignments to evaluate sequence alignments == |
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| + | === Creation of structure models from homologous sequences === |
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| + | The input for the the script hhmakemodel.pl was create with HHsearch: |
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| + | <code> |
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| + | hhsearch -i /mnt/home/student/weish/master-practical-2013/task01/refseq_BCKDHA_protein.fasta -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70_current_hhm_db -o hhsearch_BCKDHA.hhr -Z 200000 -B 200000 |
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| + | </code> |
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| + | The models were made as follows: |
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| + | <code> |
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| + | /usr/share/hhsuite/scripts/hhmakemodel.pl hhsearch_BCKDHA.hhr -d /mnt/project/pracstrucfunc13/data/pdb/20120401/entries/* -m 2 4 5 6 10 20 28 31 39 43 -ts hhmakemodel_BCKDHA.pdb |
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| + | </code> |
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| + | As can be seen in the option <code>-m</code>, 10 structures were chosen to make a model of each. The structures were selected preferably to cover the whole range of alignment scores (E-value, probability, sequence identity), but no hits with very high E-values were taken. |
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| + | The models are stored in <code>/mnt/home/student/schillerl/MasterPractical/task4/hhmakemodel/</code>. |
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| + | === Comparison with known structure === |
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| + | The models were structually aligned with the reference structure 2BDF using LGA, which was run on [http://proteinmodel.org/AS2TS/LGA/lga.html this server] with default parameters. |
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| + | LGA results can be found in <code>/mnt/home/student/schillerl/MasterPractical/task4/LGA/</code>. |
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| + | Stastitical evaluation of alignment scores (from sequence and structural alignments), especially calculation of correlation between these, was performed with R. See <code>/mnt/home/student/schillerl/MasterPractical/task4/alignment_statistics.txt</code> for an overview of the scores. |
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Revision as of 16:29, 30 May 2013
Contents
Explore structural alignments
Use structural alignments to evaluate sequence alignments
Creation of structure models from homologous sequences
The input for the the script hhmakemodel.pl was create with HHsearch:
hhsearch -i /mnt/home/student/weish/master-practical-2013/task01/refseq_BCKDHA_protein.fasta -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70_current_hhm_db -o hhsearch_BCKDHA.hhr -Z 200000 -B 200000
The models were made as follows:
/usr/share/hhsuite/scripts/hhmakemodel.pl hhsearch_BCKDHA.hhr -d /mnt/project/pracstrucfunc13/data/pdb/20120401/entries/* -m 2 4 5 6 10 20 28 31 39 43 -ts hhmakemodel_BCKDHA.pdb
As can be seen in the option -m, 10 structures were chosen to make a model of each. The structures were selected preferably to cover the whole range of alignment scores (E-value, probability, sequence identity), but no hits with very high E-values were taken.
The models are stored in /mnt/home/student/schillerl/MasterPractical/task4/hhmakemodel/.
Comparison with known structure
The models were structually aligned with the reference structure 2BDF using LGA, which was run on this server with default parameters.
LGA results can be found in /mnt/home/student/schillerl/MasterPractical/task4/LGA/.
Stastitical evaluation of alignment scores (from sequence and structural alignments), especially calculation of correlation between these, was performed with R. See /mnt/home/student/schillerl/MasterPractical/task4/alignment_statistics.txt for an overview of the scores.
