I have a list of ~200 SNPs, and am hoping to find a software that will allow me to identify what effects these variants will have on protein coding regions.
I know there are tools available through Ensembl's variant effect predictor, however I am working with an unpublished genome that does not have the resources required for these programs (coordinates for a closely related species).
Are there any tools available for simply determining if a SNP at any given locus is synonymous/non-synonymous with reference to an unpublished, non model genome?
•
written
by
sanderson •
1 answer
a SNPEFF database can be generated, for example, from a set of genbank files, from a gtf... : http://snpeff.sourceforge.net/SnpEff_manual.html#databases
Log in to answer this question.
-
Subtelomeric coordinates for the human CHM13 T2T genome in BED format
written by eusoleroliva •
-
off-target predictions to prioritize list of sgRNA designs
written by Anand Rao
-
Combined miRNA Target Prediction Algorithms for Custom Datasets/Species
written by underasail •
-
Identifying mutations in an aligment
written by Tonor
-
How to characterize synonymous and non-synonymous substitution from variants data
written by adeena_hassan •
-
How to annotate SNPs, identified against scaffolds (draft genome)
written by inayat45shaikh •
-
Snp Contig-Synonymous & Nonsynonymous
written by jackuser1979
-
Why Are There More Non-Synonymous Snps Than Synonymous Snps In The 1000 Genomes Data?
written by Ali R. Vahdati
-
Non Coding, Synonymous Snp Prediction Tool ?
written by Radhouane Aniba
-
Anyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?
written by Joe Fass
