Difference between revisions of "Gaucher Disease: Task 08 - LabJournal"

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(Chooosing Mutations)
(Chooosing Mutations)
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==Choosing Mutation set==
==Chooosing Mutations==
 
 
The cDNA sequence used by HGMD has the accession nr. NM_001005741.2). The one letter code of this cDNA has a 100% sequence identity to the reference sequence of Uniprot, which we used for all tasks. Therefore,the exact positions of the mutations listed by HGMD can be taken. The accession number is also listed by dbSNP, so that the right mutation position can be seen.
 
The cDNA sequence used by HGMD has the accession nr. NM_001005741.2). The one letter code of this cDNA has a 100% sequence identity to the reference sequence of Uniprot, which we used for all tasks. Therefore,the exact positions of the mutations listed by HGMD can be taken. The accession number is also listed by dbSNP, so that the right mutation position can be seen.
   
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For HGMD we randomly picked six mutations from the snp list of the NP_001005741.1.
 
For HGMD we randomly picked six mutations from the snp list of the NP_001005741.1.
   
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==Mutation Analysis==
 
The property information about the amino acids were taken from [http://en.wikipedia.org/wiki/Amino_acid Wikipedia].
 
The property information about the amino acids were taken from [http://en.wikipedia.org/wiki/Amino_acid Wikipedia].
   

Revision as of 09:03, 31 August 2013

Choosing Mutation set

The cDNA sequence used by HGMD has the accession nr. NM_001005741.2). The one letter code of this cDNA has a 100% sequence identity to the reference sequence of Uniprot, which we used for all tasks. Therefore,the exact positions of the mutations listed by HGMD can be taken. The accession number is also listed by dbSNP, so that the right mutation position can be seen.

To choose mutations from dbSNP we selected four point mutations of the SNP Geneview Report of glucocerebrosidase with the NP_001005741.1 which was already used in task 7. For HGMD we randomly picked six mutations from the snp list of the NP_001005741.1.

Mutation Analysis

The property information about the amino acids were taken from Wikipedia.

The visualisation of the mutations was done with pymol. For the mutation of the residues we followed the description of the PymolWiki We considered again the sequence shift of 39 residues between uniprot and pdb sequence.

We took the information about the secondary structure from our previous task 3. We alway choosed the secondary structure type which was predicted from the majority of the prediction tools in that task.

The scores for the mutations were looked up in two substitution matrices: BLOSUM62 and PAM250