I installed SequenceServer without problems on my 64 bit RHEL58 box and it seems doing something. My local install is blast2.2.27+ and I use preformatted blast databases I downloaded from NCBI. A couple remarks. It seems the only option to enter query is copy-paste, which for large files with thousands of fasta entries is very cumbersome. For a trial run I copy/pasted a file of approx. 16,000 sequences of 200 nt each, but I have files with 30,000 nt sequences. An option to upload a file from the disk, like with online BLAST, would be very useful.
It is still running, so I guess I just leave it running overnight…
Hi,
Thanks for your interest in seqserv. I’m glad your install seems to be working.
I agree, an option to upload larger fasta files would be handy. One problem this brings though is one you touched upon - the results take a long time to come back. When they are returned, you might accidentally close the window, and there is no way to retrieve your results without rerunning the entire analysis. At this stage, I can only suggest you use the command line version of blast to return and output the results to a text file, and view them there (I find ctrl-f for “Query=” makes it easy to skip between sections). If you are dealing with big input files like that, maybe you don’t want to look at them all by hand, so you might use the tabular output format so that you can manipulate the results file more easily in a spreadsheet program or programmatically.
ben