Difference between revisions of "Lab journal"

From Bioinformatikpedia
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mhc class 1 <br>
 
mhc class 1 <br>
 
<nowiki>#</nowiki> GS HFE_HUMAN/26-202 DR PDB; 1A6Z A; 4-180;
 
<nowiki>#</nowiki> GS HFE_HUMAN/26-202 DR PDB; 1A6Z A; 4-180;
 
   
 
We downloaded the alignments in fasta format. Therefore, we first formatted the alignment to fasta format and then downloaded the .txt file.
 
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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freecontact with standard parameters and evfold as output format
 
freecontact with standard parameters and evfold as output format
 
this was done with the following command:
 
this was done with the following command:
 
   
 
freecontact -o evfold < imm.aln > imm_contacts.out
 
freecontact -o evfold < imm.aln > imm_contacts.out

Revision as of 00:10, 14 June 2013

Multiple sequence alignment

The HFE protein consists of 3 domains: alpha 1 and 2 and a Immunoglobulin C1-set domain. Therefore we found two different pfam families that both match our protein: Class I Histocompatibility antigen, domains alpha 1 and 2 (http://pfam.sanger.ac.uk/family/PF07654#tabview=tab0) and Immunoglobulin C1-set domain (http://pfam.sanger.ac.uk/family/PF07654#tabview=tab0). We checked how much of out proteins sequence is covered by both fimilies: 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;

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 then formatted again 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

Calculate and analyze correlated mutations

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

Calculate structural models