Difference between revisions of "Lab journal"

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== Multiple sequence alignment ==
 
== 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 <br>
  +
<!--#-->=GS HFE_HUMAN/211-294 DR PDB; 1A6Z A; 189-272;
   
  +
mhc class 1 <br>
immunoglobulin
 
\#=GS HFE_HUMAN/211-294 DR PDB; 1A6Z A; 189-272;
+
<!--#-->=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.
mhc class 1
 
  +
The alignment were then formatted again with a2m2aln:
\#=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 < imm.txt > imm.aln

Revision as of 00:07, 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