SynBiN is a tool that allows the user to determine synonymous and non-synonymous mutations in protein coding nucleotide sequences. This is achieved by comparing the translations of query sequences to a the translation of a selected reference sequence. More than one query sequence may be uploaded at one time, and different queries can be assigned to different reference sequences.

Step 1: Upload sequences and specify translation table

Two files are uploaded. One specifying all reference sequences, the other specifying all query sequences.

• All sequences MUST be provided in the first reading frame. SynBiN translates all sequences in the first reading frame, therefore sequences provided in other reading frames will not be synchronised and will produce meaningless results.

Sequences must be in the FASTA format. Sequences in the FASTA format have the > character and the sequence name on the first line and the sequence on the following line. Several sequences can be contained in a single text file by placing them one after another e.g.

>sequence001
ACTGACTGACTGACTG
>sequence002
GTCTGTCAACTGCACT

Do not use any special characters [/ \ | @ : etc...] or spaces [replace spaces with underscores _ if necessary] in the names of your sequences

Select the translation table from the list provided. More information about translation tables can be found at the NCBI.

Step 2: Assign reference sequences

The user has the option to assign the same reference sequence to all query sequences, by ticking the box and selecting the appropriate reference...

OR

... assign a reference sequence to each individual query sequences.

Assignment of an overall reference will override individual reference-query matching.

Step 3: Results

Results are displayed as a table with the nucleotide and amino acid sequences for each reference displayed in full. Queries matched to that a reference sequence are displayed underneath and in line with the reference, with matching bases/residues marked as dots ...

• Synonymous mutations are identified where a triplet in the query sequence is shown, but no amino acid is displayed for the query at that position.
• Non-synonymous mutations are identified where a triplet in the query is shown, and an amino acid is displayed for the query at that position. The amino acid at that position in the query sequence will differ from the corresponding amino acid in the reference sequence... hence a non-synonymous mutation.

Results an be saved by highlighting the output, and copy/pasting into a text document e.g. Notepad.

Comments or suggestions regarding this service are welcome and can be sent to the author