Difference between revisions of "Lab journal"
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== Multiple sequence alignment == |
== Multiple sequence alignment == |
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| + | 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: |
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| + | 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). |
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| + | We checked how much of out proteins sequence is covered by both fimilies: |
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| + | immunoglobulin <br> |
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| + | <!--#-->=GS HFE_HUMAN/211-294 DR PDB; 1A6Z A; 189-272; |
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| + | mhc class 1 <br> |
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| − | immunoglobulin |
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| − | + | <!--#-->=GS HFE_HUMAN/26-202 DR PDB; 1A6Z A; 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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| − | mhc class 1 |
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| + | The alignment were then formatted again with a2m2aln: |
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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 |
/usr/share/freecontact/a2m2aln -q '^HFE_HUMAN/(\d+)' --quiet < imm.txt > imm.aln |
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Revision as of 23:07, 13 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
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
