Difference between revisions of "Lab journal"
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immunoglobulin |
immunoglobulin |
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| − | #=GS HFE_HUMAN/211-294 DR PDB; 1A6Z A; 189-272; |
+ | \#=GS HFE_HUMAN/211-294 DR PDB; 1A6Z A; 189-272; |
mhc class 1 |
mhc class 1 |
||
| − | #=GS HFE_HUMAN/26-202 DR PDB; 1A6Z A; 4-180; |
+ | \#=GS HFE_HUMAN/26-202 DR PDB; 1A6Z A; 4-180; |
4- 180 |
4- 180 |
||
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
