Difference between revisions of "Lab journal"

From Bioinformatikpedia
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The alignment were then formatted again with a2m2aln:
 
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 < imm.txt > imm.aln
/usr/share/freecontact/a2m2aln -q '^HFE_HUMAN/(\d+)' --quiet < mhc.txt > mhc.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
+
/usr/share/freecontact/a2m2aln -q '^RASH_HUMAN/(\d+)' --quiet < ras.txt > ras.aln
   
 
== Calculate and analyze correlated mutations ==
 
== Calculate and analyze correlated mutations ==
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freecontact -o evfold < imm.aln > imm_contacts.out
+
freecontact -o evfold < imm.aln > imm_contacts.out
freecontact -o evfold < mhc.aln > mhc_contacts.out
+
freecontact -o evfold < mhc.aln > mhc_contacts.out
freecontact -o evfold < ras.aln > ras_contacts.out
+
freecontact -o evfold < ras.aln > ras_contacts.out
   
 
== Calculate structural models ==
 
== Calculate structural models ==

Revision as of 00:09, 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