[Bioperl-l] best way to edit sequence features

[Roy Chaudhuri]

The Sanger Institute's Artemis is good for editing sequence features, 
and DNAPlotter can be used to produce circular diagrams:

http://www.sanger.ac.uk/resources/software/artemis
http://www.sanger.ac.uk/resources/software/dnaplotter

Roy.

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,
> 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
>
>
>
> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l