How To Get The Coding Sequences (Cds) Based On The Protein Aminoacid Sequence

Question

[harrymao20]

Now I have protein (NCBI) NP_391988.1 ,and its mRNA file NM_033668.2,how can i get the CDS correspond to the Protein sequence

[Pierre Lindenbaum]

if you have the aminoacid sequence, you have the CDS.

Answer 1

[Gabriel R.]

go to ncbi:

http://www.ncbi.nlm.nih.gov/nuccore/NM_033668?report=GenBank

1. next to Send: click on the arrow.
2. click on coding sequence
3. make sure fasta nucleotide is checked
4. download

Answer 2

[seancho]

The most straight forward method is what Gabriel R. has suggested. The alternative, which allows documenting it at the same time, is to do so from the command line via Edirect.

esearch -db nucleotide -query "NM_033668.2" | efetch -format fasta_cds_na > cds_nm033668-2.fasta

Answer 3

[Ibrahim Tanyalcin]

You can use a software we have recently published I-PV (http://i-pv.org/). You will need perl and circos installed to be able to use it. It needs an mRNA sequence and a fasta file of your protein sequence ( the one that starts with NP_...). It will automatically generate a protein graph for your CDS. You can than compare each aminoacid and its codon...etc

Answer 4

[Maximilian Haeussler]

Click View - DNA in the UCSC Genome Browser, search for your identifiers, click on the transcript and click "Get Protein sequence".