Question: How To Get The Coding Sequences (Cds) Based On The Protein Aminoacid Sequence
gravatar for harrymao20
5.7 years ago by
harrymao200 wrote:

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

cds • 3.5k views
ADD COMMENTlink modified 23 months ago by seancho40 • written 5.7 years ago by harrymao200

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

ADD REPLYlink written 5.7 years ago by Pierre Lindenbaum116k
gravatar for Gabriel R.
5.7 years ago by
Gabriel R.2.5k
Center for Geogenetik Københavns Universitet
Gabriel R.2.5k wrote:

go to ncbi:

  1. next to Send: click on the arrow.
  2. click on coding sequence
  3. make sure fasta nucleotide is checked
  4. download
ADD COMMENTlink written 5.7 years ago by Gabriel R.2.5k
gravatar for seancho
23 months ago by
seancho40 wrote:

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
ADD COMMENTlink written 23 months ago by seancho40
gravatar for Ibrahim Tanyalcin
3.3 years ago by
Ibrahim Tanyalcin920 wrote:

You can use a software we have recently published I-PV ( 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

ADD COMMENTlink written 3.3 years ago by Ibrahim Tanyalcin920
gravatar for Maximilian Haeussler
23 months ago by
Maximilian Haeussler1.3k wrote:

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

ADD COMMENTlink written 23 months ago by Maximilian Haeussler1.3k
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