DNA translation for publication

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iruka
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DNA translation for publication

Post by iruka » Tue Apr 22, 2008 1:57 pm

Hello!

Does anyone know any software that shows DNA translation aa aligned with nucleotides nicely for publication?

Thanks!

Iruka

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mith
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Post by mith » Tue Apr 22, 2008 5:11 pm

one of my profs uses macclade
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snowcapk
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Post by snowcapk » Tue Apr 22, 2008 9:13 pm

Hi Iruka,

A figure like the one you've described consumes a lot of space. Make one if you like, but the publisher may well ask you to remove it or place it in the SOM. Journals like Science are on a mission to save space: they don't even let you include article titles in your references section.

Most journals expect you to submit your sequence (assuming it's new) to a database like GenBank, and refer to the accession number in the body of the manuscript. Since the GenBank entry can contain both the sequence and its translation, as well as a variety of annotations, there is no reason for you to list your nucleotide sequence and its translation in a figure. You can just describe features of the sequence with reference to GenBank for the curious.

Maybe you were planning on describing the location of aas that you mutated or deleted? This can be represented in much less space using a "stick diagram": you draw a stick, draw in some features, and then mutate or delete using Xs or Vs (like this).

I don't know any programs that align sequence and translation "nicely" (macclade looks so...colorful) - I think part of it is that this just isn't "done" for publication purposes these days.

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Re: DNA translation for publication

Post by blcr11 » Wed Apr 23, 2008 12:43 pm

You can try ESPript for pretty pictures of aligned sequences. You can get a similar thing out of Blast, but I don't think you have the option for showing secondary structure, if it is known. I could be wrong about that, though.

Here is the ESPript link. It's most easily used as a web service, but you can install a standalone version.

http://espript.ibcp.fr//ESPript/ESPript/

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