I want to know that is there is any suitable tool for extracting start codon and stop codon from the fasta file of multiple protein-coding genes (PCGs). I have downloaded multifasta PCGs (nucleotides) from NCBI; now I want to get the start codon and stop codons of all fasta sequence at a go. Thanks in advance.
I have used Expasy's TRANSLATE for single sequences. However you could try http://www.ebi.ac.uk/Tools/st/emboss_transeq/
Oh thanks, Imah Mwaba for the reply... Actually, I'm not looking for translation; Exactly what I have need is that particularly the start codon and the stop codon of the nucleotide sequence which is obviously a protein-coding gene.
Sequence in your file doesn't start with start codon ?
Is it ATG position you need or just 'ATG' ? (same for stop codon)
I think we need more information to help.
I have started using PAL2NAL server for getting the Start and Stop codons, but it will be very good if I get a more sophisticated tool. Thanks everyone for participating in the discussion.
As the information you provided you have the fasta sequence file then you can just translate it by any online tool like EXPASY, you will get the translated sequence and then you can get the any longest amino acid sequence with out any stop codon then count the methionine amino acid number and then you can get the location of ATG(start codon) and stop codon.
hope you get this..
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