display orientation of sequences in alignment

[azim58]

How can I display the orientation of sequences in a blast alignment? In particular, I am using Bl2seq to align multiple sequencing results and primers, and I would like to be able to quickly see the orientation of the aligned sequences and primers. Is there a way to do this from the BLAST website. Is there some other tool that will do this (preferably a free one)?

[WhatsOEver]

If you use the NCBI Blast2sequences website, you already get the orientation together with the alignment. Above the alignments you have "Score Expect Identities Gaps Strand". The strand corresponds to the orientation: plus = forward, minus = reverse. If it reads "plus/minus" your query sequence is forward, the subject sequence reverse.

[azim58]

However, I was hoping for a visual graphic which displayed the orientation up at the top where the graphic is. I think this feature is not available.

[WhatsOEver]

Maybe the "Dot Matrix View" (beneath the graphic summary) is what you are looking for. If the slope of a line is ascending, both sequences match on the same strand, if it is descending, they match on opposite strands.

[azim58]

The "Dot Matrix View" is only available if there is just one subject sequence. I was also hoping for more of a graphic that shows lines for each sequence with a forward or reverse arrow for each line. Thanks for the suggestion though.

[WhatsOEver]

Ok, one last try before I give up
Is the organism you are working with available at the JGI database?
Because their Blast output has arrows to indicate orientations. You will, however, be restricted to one organism (but as you mentioned primer alignment you're probably only interested in one?!)

[gringer]

JBrowse will display read direction combined with read number, but it's a little bit of a mission to set up.