Editing Contigs Browser

Question

[Biojl]

Hi,

I was wondering if anyone knows of an easy web browser application/code that I could use to show small contigs/alignments (few Kb) and ideally allow editing, modifying the original file (or a copy).

Thanks.

Answer 1

[Pierre Lindenbaum]

"modifying the original" you meant the image ?

You could just encode your contigs as XML and transform it with XSLT to produce a SVG file. See that example with the UCSC data (2006) : http://plindenbaum.blogspot.fr/2006/02/ucsc-genome-browser-svg.html

and that previous post:

Batch Viewing of UCSC Browser Graphic

and that one : a Local file that can be edited; http://plindenbaum.blogspot.fr/2010/08/tiny-genome-browser-xhtmljavascriptjson.html

[Biojl]

By modifying the original I mean editing the alignment and changing the original file (fasta, phyllip...) if the user deletes an indel or moves a nucleotide.

Answer 2

[jackuser1979]

If you are familiar with Gbrowse, you can use Jbrowse and you can embed in your webpage.