Question: How to add translation of CDS in Artemis?
gravatar for Audrey
4 days ago by
Audrey20 wrote:

Hi all,

I am trying to add the translated protein sequence on the "Artemis Feature Edit: CDS" but I don't know how. When I go to "Add Qualifer" section I can not find "/translation" therefore I can not add the amino acid sequence of the protein.

I didn't find this information on the artemis user guide.

Could you help me please?

Thank you so much in advance

/translation artemis • 45 views
ADD COMMENTlink written 4 days ago by Audrey20

Can you explain in a bit more detail what exactly you want to achieve here? The CDS translation is depicted in the track view with the aminoacids, so unless the translation of that specific CDS deviates from the general rules (eg. Selenocysteine proteins, ...), there is no need to specifically add the translation

ADD REPLYlink written 4 days ago by lieven.sterck9.4k

Thank you for your reply.

I want to have a genbank file looking like this (example):

/locus_tag="CS400_15500" /inference="COORDINATES: similar to AA sequence:RefSeq:YP_133737.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="ATQ35059.1" /translation="MKKIAHWLLEKAKKDMRTDPFTTPSRRTKLSYYFDNLVSMVFYI MGIYLMLMDLYQELFTANHTDFLGTALMALVLLLGGLLFRWSAYADLKAINRYQHYLK QQSIEQQQELRRETWLKAAKQGKTELDQKLNHKE"

I am not able to add the /translation ...

Is it clearer ?

ADD REPLYlink written 4 days ago by Audrey20

if you need/can do this in a automated way than perhaps here you can find an approach for doing so: adding fields to a genbank (translation)

In a manual way, you can do the following: go to the edit vie of that CDS, at the top in the 'add qualifier' menu, select 'translation', then click the 'add qualifier'. doing so the /translation="" will appear in the edit field below. Now you can paste your translation in between the "" and save it.

ADD REPLYlink modified 4 days ago • written 4 days ago by lieven.sterck9.4k
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