I am working on a database for the non AUG codons and I have a fasta file that i downloaded from refseq from an automated perl script. Now I want to check each and every sequence Individually of that file for the CDS region that have alternate translation initiation and hence print the Accession number from the header file.
To check the Alternate Initiation we need to check for the Kozak Context. -3 should be a purine and +4 a Guanine.
eg. AATAACTGGTTA. Counting from C at -3 is a purine and +4 is A G !
I'm new to perl programming. Can anyone help me ?
And I don't wana use Bioperl so !
Thanks in Advance !