Tool For Visualizing Sections Of Sequences

Question

[Michele Busby]

Hello,

I am looking for a tool to help me visualize the position of adapters in a bunch of Sanger sequences.

So I have a FASTA file containing the sequence. Each sequence will contain between 0-5 different known adapter sequences. I just want to display where they are easily.

I can identify them and put the annotation into what file format the tool wants.

I can write something easily enough but it seems like I would surely be reinventing the wheel. I just want something basic.

Any suggestions for this sort of work?

Thank you!

Michele

Answer 1

[Damian Kao]

I wrote a tool recently that let's you visualize features of sequences: http://www.nextgenetics.net/tools/anno_view/annotator.html

It might be buggy so let me know if you have any problems with it. You just need to paste your data in tab delimited format like so with 5 columns: sequence name, feature name, start position, end position, sequence length. Here are some sample data:

sanger01    adapter01    20    50    400
sanger01    adapter02    200    220    400
sanger02    adapter01    10    40    500
sanger03    adapter02    60    80    300

[Michele Busby]

Great! I'll give it a try. Thank you!