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

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(Chooosing Mutations)
(Chooosing Mutations)
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==Chooosing Mutations==
 
==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.
   
 
To choose mutations from dbSNP we searched for non-synonymous snps and took the first five snp entries:
 
To choose mutations from dbSNP we searched for non-synonymous snps and took the first five snp entries:
 
"missense"[Function_Class] AND GBA[GENE] AND "human"[ORGN] AND "snp"[SNP_CLASS]
 
"missense"[Function_Class] AND GBA[GENE] AND "human"[ORGN] AND "snp"[SNP_CLASS]
   
For HGMD we randomly picked five mutations from the snp list of the NM_001005741.2.
+
For HGMD we randomly picked six mutations from the snp list of the NM_001005741.2.
  +
  +
We took the information about the secondary structure from our previous [ https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Gaucher_Disease:_Task_03_-_Sequence-based_predictions#Human_Glucosylceramidase_.28P04062.29 task 3]. We alway choosed the secondary structure type which was predicted from the majority of the prediction tools in that task.

Revision as of 21:52, 30 August 2013

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.

To choose mutations from dbSNP we searched for non-synonymous snps and took the first five snp entries:

"missense"[Function_Class] AND GBA[GENE] AND "human"[ORGN] AND "snp"[SNP_CLASS]

For HGMD we randomly picked six mutations from the snp list of the NM_001005741.2.

We took the information about the secondary structure from our previous [ https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Gaucher_Disease:_Task_03_-_Sequence-based_predictions#Human_Glucosylceramidase_.28P04062.29 task 3]. We alway choosed the secondary structure type which was predicted from the majority of the prediction tools in that task.