I have some sequencing results I want to blast in order to identify what are known SNPs and what are not and which variations lead to which effect (synonymous or non-synonymous mutation) ? At the end, I want a file with a single Refseq transcript ID (preferably the longest transcript) and all the variations identified for this gene with, for each SNP the indication of the position (coding / non-coding), the consequence (synonymous/non-synonymous) the amino acid substitution etc..
In order to do this I used the SIFT tool on my results. But this latter, seems to choose randomly the transcript sequence he's referring to. For example, when I enter this variations
I have a second problem related to the same field. This I've got multiple output Ensembl transcript ID for the same gene with the SIFT tool, I tried the AAchange one.Once I had the results, I compared them with the one I had with the SIFT tool. Surprisingly, I found a systematic decay in the mutated codon between this 2 tools ! I check 1 or 2 identified SNPs found with the SIFT tool to see what was the good results and according to the DbSNP database it appears that the SIFT tool is right even if he doesn't always consider the refseq transcript. So my question is why do they identy different affected codon (even when they used the same transcript) and how I can force the AAchange tool to start the analysis at the good nucleotide (to get rid of the decay) ?
If it can help you I enclosed the link allowing you to see what I did and what I get :http://main.g2.bx.psu.edu/u/charlotte/h/sift-vs-aa-change
If you could help me on this issues it would be great for me ( my work and my boss)!
Charlotte Gueydan , PhD.
INSERM/Université Pierre et Marie Curie
Hôpital Tenon - bâtiment de recherche
4, rue de la Chine
75020 Paris cedex 20
tel : 01 56 01 83 75
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