Genetic Code Alteration - blastx

[SHeaph]

Hi All,

I'm not sure if I'm in the right forum with this query. But any info would be great!

I am running blastx on a standalone version of blast-2.2.31+. Using the standard genetic code each stop codon (TAA, TAG, TGA) is represented by the asterisk symbol '*'.

Is it possible to amend the genetic code to give each stop codon an individual symbol? for example TAA '#', TAG '&', TGA '%'

Is it possible to supply a uniquely generated genetic code to standalone blastx searches?

I have read through the literature and have not found examples of such amendments.

[maubp]

You can use some of the predefined genetic code tables defined by the NCBI,

$ blastx -help
...
 -query_gencode <Integer, values between: 1-6, 9-16, 21-25>
   Genetic code to use to translate query (see user manual for details)
...

See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

Defining your own would probably required editing the BLAST+ source code and making your own modified blastx tool (i.e. theoretically possible but not easy).

[GenoMax]

Just speculating. It may be easier to check the sequence in the blast hits to differentiate the three codons?

[SHeaph]

Thanks for the suggestion. I'm performing multiple sequence alignments with large data sets >50,000 sequences and hoping to identify stop codon reassignments. However all three stop codons are identified by the '*' symbol so I can't tell them apart.

[maubp]

In your case I could think about writing some custom scripts to take the BLAST output and original nucleotide sequences, and map the stop codons to three different symbols.

(If you are not already, you should think about learning a programming language to help with your research - check out Software Carpentry workshops etc.)