Question: How to extract start codon and stop codon from a fasta of multiple protein coding genes !
0
gravatar for kabir.deb0353
2.0 years ago by
kabir.deb03530 wrote:

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.

stop codon start codon • 1.3k views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by kabir.deb03530

Seems just get the first 3 bases or last 3 bases from CDs sequences?

ADD REPLYlink written 2.0 years ago by shenwei3564.5k

ORFfinder

ADD REPLYlink written 2.0 years ago by st.ph.n2.4k

Yes, first 3 bases for Start codon and last 3, 2, or 1 base for the Stop codon; because some of the nucleotide seq have the cryptic stop codons. So the logic is that it will start count as 3 bases from beginning and print the first three letter of the sequence and then it will count upto to the second last codon and print the remaining bases as stop codon.

Sample ATG GGC TAT CGT TAC GAT TAC AGT ACC T

So, Here the probable output will be Start codon: ATG Stop codon: T

ADD REPLYlink written 2.0 years ago by kabir.deb03530

Please use ADD COMMENT to reply to earlier reactions, as such this thread remains logically structured and easy to follow. I have now moved your post, but as you can see it's not optimal.

ADD REPLYlink written 2.0 years ago by WouterDeCoster38k

Yes, first 3 bases for Start codon and last 3, 2, or 1 base for the Stop codon; because some of the nucleotide seq have the cryptic stop codons. So the logic is that it will start count as 3 bases from beginning and print the first three letter of the sequence and then it will count upto to the second last codon and print the remaining bases as stop codon.

Sample ATG GGC TAT CGT TAC GAT TAC AGT ACC T

So, Here the probable output will be Start codon: ATG Stop codon: T

ADD REPLYlink written 2.0 years ago by kabir.deb03530
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 695 users visited in the last hour