sequence viewer

[Quat]

Hello,

I've been looking around for a while for a visual sequence viewer to replace notepad++ without much luck. The key features I'm interested in are being able to load a fasta file (scaffold/chromosome size hopefully), and being able to either import and view blast alignments, or provide other files for a blast alignment, being able to view coordinates from the match and being able to provide coordinates and extract a sub-sequence from the large fasta file to work with.

Is there a simple program which fits this bill?

Thanks

[bio_boris]

Have you tried BioEdit? It may have some of the features you are looking for.

[Quat]

thanks, bioedit is pretty close to what I want and will make things easier.
hoping to find an editor which will display blast results on a sequence visually.

if I give it a scaffold as the subject and then blast a coding sequence against the scaffold, I'd like to see the hits laid out on the scaffold.

[bio_boris]

Doesn't blast give you that information in standard mode?

[Quat]

I'm not sure what you mean, what I'm familiar with is local blast gives alignments like this:

Query: 403     AQVFHFCI---FGNRLIEESSSVMEAAYSCHWYDGSEEAKTFVQIVCQQCQKAMSISGAK 459
               + +F F I      +L  +SSSVMEAAYSCHWYDGSEEAKTFVQIVCQQCQK++++SGAK
Sbjct: 3261942 SMLFFFVICKQLSTQLQFQSSSVMEAAYSCHWYDGSEEAKTFVQIVCQQCQKSLTVSGAK 3261763

Which are useful, but what I'd like is to be able to see the whole subject strand with the alignments mapped so that I can see possible intron/exon structure easily.

[amitm]

hi Quat,
have you tried Jalview. http://www.jalview.org/
It does very well representation of .aln files

[Quat]

I hadn't tried jalview, it looks interesting.