[Bioperl-l] best way to edit sequence features

Carnë Draug carandraug+dev at gmail.com
Tue Nov 1 11:13:06 EDT 2011

On 1 November 2011 10:18, Hotz, Hans-Rudolf <hrh at fmi.ch> wrote:
> I am aware of the following ones (as far as I know, they are all GUI based
> and don't have a command line API):

They are not all free. Just for future reference, here's their licenses:

> Serial Cloner

Couldn't find a license and the download for linux has no source so
I'm guessing proprietary.

> GENtle            http://gentle.magnusmanske.de/

Free under GPL

> GeneCoder


> pDRAW32


> Genome Workbench  http://www.ncbi.nlm.nih.gov/projects/gbench/

Seems public domain. License is not defined anywhere but the files I
checked had the public domain notice on the header

> Ape

Proprietary ("license" is at the top of AppMain.tcl)

> UGene             http://ugene.unipro.ru/

Free under GPL

> Also, have you looked at the emboss tool "cirdna" ?

Free under GPL

> WRT file formats: I strongly suggest to stick to embl and genbank format as
> input and (text) output format. The features are not indexed, but you can
> create your own when you store the sequences in your system. Internally, you
> probably wanna keep the data in a 'simpler' format than embl or genbank,
> anyway.
> Alternatively, have you looked at gff/gtf as away of getting features?
> see:
> http://www.sequenceontology.org/gff3.shtml
> http://mblab.wustl.edu/GTF22.html

Considering the already existing alternatives, I'm more likely to
collaborate with one of them to do what I want. I'll just have to
check them all and decide. I was planning on writing a new tool and
contribute it to the scripts section of bioperl since when I googled
before all the links only the proprietary tools showed up. Thank you
very much for the links.


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