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[Software] Drawing arrows as ORFs on genes


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6 replies to this topic

#1 fastaman

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Posted 02 November 2010 - 04:50 PM

Hi all,

I've been searching the last few days for a software (preferably free) that could draw the arrows that represent ORFs on genes. I have multiple contigs from different bacteria with some ORFs of interest that I would like to draw all together vertically so I can compare these regions between them.

I know I could probably do that on Powerpoint, but I'm sure there is a program somewhere which, given the nucleotide positions of the orfs, could draw them more precisely. I have found one named "FancyGene" (http://host13.bioinf...s.it/fancygene/), but it only draws exons and introns on eukaryotic genes, which is not quite what I need, since the arrows I want to draw are both on the sense and anti-sense strand.

I was expecting something like this picture: http://img688.images...creenshotkc.png

Posted Image

Thanks!
P.

#2 bob1

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Excellent

Posted 06 November 2010 - 02:25 PM

Try ApE (A plasmid editor) which is freeware.

#3 pDNA

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Posted 07 November 2010 - 12:16 AM

pDraw32 will also be a good choice.

You can display your stretch of DNA circular or linear. The programm will find ORFs and you can annotate them ...and color the arrows the way you like it most.

You can finde the programm here.

Regards,
p

#4 fastaman

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Posted 09 November 2010 - 06:01 AM

Thank you, guys, I'm installing both of them right now to see which is better.

May the plasmid be with you,
P.

#5 feilr

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Posted 16 December 2010 - 12:42 AM

NoeClone also be a good choice
you can display your stretch of DNA circular or linear. The programm will find ORFs and you can annotate them ...and color the arrows the way you like it most. And aslo some other functions.
http://www.noegen.co...oduct_clone.php

#6 bglick

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Posted 28 April 2012 - 09:21 AM

SnapGene Viewer (free for Mac and Windows) has a nice modern interface that allows you to display translated features. The program is very easy to use. You can see the features as colored arrows in Map view, and you can see the translations in Sequence view. Translated features can be shown in either direction, and introns can be annotated.

http://www.snapgene....napgene_viewer/

#7 branthackett

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Posted 19 September 2014 - 08:53 AM

Gene Construction Kit® (GCK) is also a useful tool for plasmid mapping, cloning simulation, and DNA analysis. It has been consistently reviewed as being one of the easiest to use applications for simulating multi-step cloning operations, and offers extensive flexibility in the graphical formatting of DNA sequences - and - identifying ORF's. The ORF indicators can be selected, and customized to your liking (changing directions, colors, line thickness, fill paterns, even the size of the arrow heads). You can easily copy and paste grapical maps from GCK to image editing programs, or even create hi-res PDF (Mac) or XPS (Win) exports from within the program. It's been around since the mid-90's, and was one of, if not "the very first software" for performing these types of graphical manipulations of DNA sequence data.

 

More information, and a free demo version is available from the website: http://www.textco.com

 

Check it out!

 

 

Attached Thumbnails

  • GCK40-LinearMap.jpg

Edited by branthackett, 19 September 2014 - 08:54 AM.





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