[Bioperl-l] best way to edit sequence features

Hotz, Hans-Rudolf hrh at fmi.ch
Tue Nov 1 06:18:54 EDT 2011

Hi Carnë

Please allow me to make a few comments:

I very much like your idea of writing a free tool to edit and draw
sequences. We (ie people working in core Bioinformatics facilities) all
suffer from having to deal with files originally created with commercial
packages. And on top of all the pain, those commercial packages are very
expensive and they don't deliver what they promise to do.

Just double checking: Have you looked a the free tools which are available?

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):

Serial Cloner     http://serialbasics.free.fr/Serial_Cloner.html
GENtle            http://gentle.magnusmanske.de/
GeneCoder         http://www.algosome.com/gene-coder/gene-coder.html
pDRAW32           http://www.acaclone.com/
Genome Workbench  http://www.ncbi.nlm.nih.gov/projects/gbench/
Ape               http://www.biology.utah.edu/jorgensen/wayned/ape/>
UGene             http://ugene.unipro.ru/

maybe others on the list know of even better free tools?

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

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,

Alternatively, have you looked at gff/gtf as away of getting features?


I am looking forward to any progress you make

Regards, Hans

Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland

On 10/31/11 7:05 PM, "Carnë Draug" <carandraug+dev at gmail.com> wrote:

> Hi
> I've been planning on writing a free (as in freedom) tool to edit
> sequences and make plamids maps. The idea is to build the command line
> tool first and maybe later work on a GUI for it.
> The problem I foresee at the moment while designing it, is how to
> change a feature of the sequence. I'm not familiar with all sequence
> formats (only fasta, ensembl and genbank) but I can't see how to
> specify from the command line what feature to edit since I can't see
> any unique identifiers for them. Is there a file format that makes
> this easier? Any tips would be most appreciated.
> Thank in advance,
> Carnë Draug
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