Question: Aachange And Sift Tools
0
Charlotte Gueydan • 20 wrote:
Hello,
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
chr19 39191323 + C/T
chr19 39191733 + C/T
chr19 39195653 + C/T
chr19 39196688 + C/T
chr19 39196736 + G/A
chr19 39196745 + C/T
chr19 39207742 + G/A
chr19 39214633 + C/T
chr19 39215172 + T/C
chr19 39215193 + G/A
chr19 39218649 + G/A
chr19 39219780 + T/C
chr19 39220016 + G/A
chr19 39220279 + A/T
the SIFT tool identifies 13 SNPs in the transcript ENST00000252699 (9
novel and 4 already known) and 1 in the ENST00000445727 but this
referring to the same gene : ACTN4! I don't understand why is this
happening and how can I force SIFT tool to "blast" the SNP on only one
transcript (preferably the one corresponding to the longest isoform) ?
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
<http: main.g2.bx.psu.edu="" history="" sharing?id="dbac2dd575f62542#">
If you could help me on this issues it would be great for me ( my work
and my boss)!
thanks
Charlotte
*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