blast against between two sequence (database sequence path is variable based on user input in server


First of all I appreciate your work. This is really helpfull for biologists.
I want to implement sequence server in my web-server for displaying alignment between different sequences.
I have one sequence as a query and other one is as a Database(only two sequence).
Location of file contain these two sequence varies each time i.e database sequence is not fixed.
How can I display alignment between these two using sequence-server.

I will appreciate your help.



This sounds like a pairwise BLAST. You could consider using -subject option of BLAST or dynamically format the target sequences into a BLAST database.

I would suggest the latter approach. You will be able to leverage SequenceServer for creating database and loading them into the search form. There’s also small difference b/w the two approaches with regards to the output. Peter Cock touches on it in his blog Blasted Bioinformatics!?.

Regarding your target sequences always changing location, you will have to find some way around that.

Overall, I think you can build around SequenceServer like so:

this keeps changing

$ target_sequences="/some/directory"

create database from target sequences. Will need to figure out a way to make this non-interactive.

$ sequenceserver -m -d $target_sequences

change database dir in config file

$ sequenceserver -s -d $target_sequences

ask Apache+Passenger to restart SequenceServer. See Phusion Passenger’s manual for more information

$ touch /seqserver/install/dir/tmp/restart.txt

Then based on some event or information of how the directory that contains target sequences changes, you just run this script and loading the page will contain new target sequences / databases now.

I hope this helps.

P.S: Our AGPL license probably requires you to release this code publicly. Based on your requirements, please feel free to contact us off the list for other licensing option.

– Priyam