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
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