Diamond In SequenceServer

sequenceserver
#1

Hi,

I am looking for a interface that will run Diamond sequence alignment routine. The paper (https://www.biorxiv.org/content/10.1101/033142v1.full) stated that the sequenceserver team is planing to integrate Diamond into their program in the future. I was wondering whether it has been incorporated into it yet. If not, are there any other web user interfaces that incorporates Diamond?

Thank you,
Harikumar K

#2

Hi Harikumar,

We have been working on few things with sequenceserver recently, including ability to import XML reports and use SequenceServer to visualise them. At the moment the feature seems to be working great, however we are still testing it to avoid any issues with it in the future. SequenceServer was tested with diamond blastp and blastx XML reports and everything worked amazingly well. Usage of the feature is pretty simple as it requires running SequenceServer with this command:

bundler exec bin/sequenceserver --import “PATH/TO/THE/FILE”

which will generate a string of numbers and letters which are described as uuid in the code and to be pasted in the browser as localhost:4567/. This will be able to present XML reports of any BLAST algorithm from version 2.2.30-2.9.0 and from diamond outpts - version 0.9.24 has been tested.

If you would be interested in using this feature before the official release of a new version (which should happen by September) please let us know either here or on ivo.pieniak@gmail.com

Thank you,
Iwo Pieniak

#3

Hi,

I forgot to mention that mentioned ability to import XML reports from DIAMOND is already available on the master branch on sequenceserver github.

https://github.com/wurmlab/sequenceserver

Regards,

Iwo Pieniak

#4

Dear Iwo Pieniak,

Thank you so much for the information. I shall wait till September for the official release to use this feature. I really appreciate the link to master branch of sequenceserver GitHub page and i will check it out. I am not that good at playing with source codes myself but hopefully i do have a few friends who can help me with it.

Thank you,

Regards,
Harikumar K