Obtain information on non-synonymous (nsSNPs) and functional SNPs (fSNPs)

From this page you can search for SNPs that produce a non-synonymous (missense) mutation and obtain information on the sequence surrounding the SNP, the amino acid sequence and annotations.

A non-synonymous mutation is a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid. These mutations can render the resulting protein non-functional, however the amino acid substitution with another amino acid with similar chemical properties can result in a neutral mutation and the protein will function normally.

Functional SNPs are non-synonymous SNPs that have a deleterious effect on protein function. The fSNPs in CerealsDB have been characterised using the FATHMM pipeline (Shihab et al.) and annotated with BLAST against a non-redundant embryophyta database.

Functional SNPs are defined as SNPs with a FATHMM score less than -3.0 or greater than 3.0.

Using the input fields below you can access fSNP information in several different ways:

1) Enter a SNP name (a 10 character alphanumeric beginning with 'BS' or 'BA'; e.g., BS00010624 or BA0033400) to find the contig to which it maps and all other putative SNPs, validated or not, that have been mapped to it. SNP names (IDs) may take different forms depending on the platform on which the assay was developed:

KASP assays BS00003890
Axiom array BA00809142

SNP names with 'BS' codes may have an extention (e.g., '.1', '.2'. These should not be added when performing a search; if they are added they will be removed by the program before the search is performed.

2) Enter a search term (e.g., disease) in order to obtain a list of contigs that when BLASTed against the NCBI database returned a hit containing the chosen term.

3) Set a threshold for the FATHMM score (e.g. -3 will return all SNPs with a FATHMM score less than -3.0)

4) Set a threshold for the FATHMM score (e.g. 3.0 will return all SNPs with a FATHMM score greater than 3.0)

1) SNP_id (e.g. BS00003890 or BA00809142) 
2) Search term (e.g., 'disease', 'glutenin') 
3) FATHMM score LESS THAN (e.g. '-3' ) 
4) FATHMM score GREATER THAN (e.g. '3.0') 

Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon