Difference between revisions of "Lab journal"
From Bioinformatikpedia
(Created page with " == Multiple sequence alignment == == Calculate and analyze correlated mutations == == Calculate structural models ==") |
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== Multiple sequence alignment == |
== Multiple sequence alignment == |
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| + | immunoglobulin |
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| + | #=GS HFE_HUMAN/211-294 DR PDB; 1A6Z A; 189-272; |
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| + | |||
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| + | mhc class 1 |
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| + | #=GS HFE_HUMAN/26-202 DR PDB; 1A6Z A; 4-180; |
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| + | 4- 180 |
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| + | |||
| + | we downloaded the alignments in fasta format. Therefore, we first formatted the alignment to fasta format and then downloaded the .txt file. |
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| + | The alignment were formatted with a2m2aln: |
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| + | |||
| + | /usr/share/freecontact/a2m2aln -q '^HFE_HUMAN/(\d+)' --quiet < imm.txt > imm.aln |
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| + | /usr/share/freecontact/a2m2aln -q '^HFE_HUMAN/(\d+)' --quiet < mhc.txt > mhc.aln |
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| + | /usr/share/freecontact/a2m2aln -q '^RASH_HUMAN/(\d+)' --quiet < ras.txt > ras.aln |
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== Calculate and analyze correlated mutations == |
== Calculate and analyze correlated mutations == |
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| + | |||
| + | freecontact with standard parameters and evfold as output format |
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| + | this was done with the following command: |
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| + | |||
| + | |||
| + | freecontact -o evfold < imm.aln > imm_contacts.out |
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| + | freecontact -o evfold < mhc.aln > mhc_contacts.out |
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| + | freecontact -o evfold < ras.aln > ras_contacts.out |
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== Calculate structural models == |
== Calculate structural models == |
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Revision as of 23:00, 13 June 2013
Multiple sequence alignment
immunoglobulin
- =GS HFE_HUMAN/211-294 DR PDB; 1A6Z A; 189-272;
mhc class 1
- =GS HFE_HUMAN/26-202 DR PDB; 1A6Z A; 4-180;
4- 180
we downloaded the alignments in fasta format. Therefore, we first formatted the alignment to fasta format and then downloaded the .txt file. The alignment were formatted with a2m2aln:
/usr/share/freecontact/a2m2aln -q '^HFE_HUMAN/(\d+)' --quiet < imm.txt > imm.aln /usr/share/freecontact/a2m2aln -q '^HFE_HUMAN/(\d+)' --quiet < mhc.txt > mhc.aln /usr/share/freecontact/a2m2aln -q '^RASH_HUMAN/(\d+)' --quiet < ras.txt > ras.aln
freecontact with standard parameters and evfold as output format this was done with the following command:
freecontact -o evfold < imm.aln > imm_contacts.out
freecontact -o evfold < mhc.aln > mhc_contacts.out
freecontact -o evfold < ras.aln > ras_contacts.out
