[Bioperl-l] best way to edit sequence features
roy.chaudhuri at gmail.com
Tue Nov 1 11:44:19 EDT 2011
The Sanger Institute's Artemis is good for editing sequence features,
and DNAPlotter can be used to produce circular diagrams:
On 01/11/2011 10:18, Hotz, Hans-Rudolf wrote:
> 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:
>> 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
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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