Forum:Sequenceserver: Easily Deploy A Custom, User-Friendly Blast Webserver

Question

[Yannick Wurm]

Executive Summary: SequenceServer lets you rapidly set up a custom BLAST+ server with an intuitive user interface for use locally or over the web.

Why we created it: We were frustrated with:

1. Too many colleagues asking: can you BLAST this for me?
2. Installing NCBI's wwwblast is too complicated and the user interface is unnecessarily counter-intuitive.

So we created something better that tries to overcome both hurdles. We try to make it real easy to install, and idiot-proof for users (still some progress to be made but we're on the right track!). Complete overview.

Installation: Takes 5 minutes:

1. gem install sequenceserver
2. sequenceservernow guides you through configuration, downloads necessary binaries & launches the server on http://localhost:4567/

Demo Servers: We know it is deployed in >40 institutions. Our deployment is antgenomes.org.

Check it out & let us know if any questions. It's open source on GitHub.

Edit: Preprint manuscript on biorxiv

[JacobS]

Just want to put my 2 cents in here... I found and used SequenceServer a couple years ago for allowing colleagues to easily BLAST unmapped contigs after a genome assembly. They weren't interested in learning UNIX commands to BLAST like the rest of us, and the GUI on SequenceServer was both easy to set up and visually impressive to use. I even cited it in my thesis! So props to the author.

[Yannick Wurm]

Thanks for the plug Jacob - glad it is/was useful :)

[Richard Smith-Unna]

We're also using SequenceServer on the C4 rice project and with data from 1KP to offer BLASTing against out de-novo transcriptome assemblies. It's extremely easy to install. Plus it's in Ruby, so easy to modify :). I'm planning to throw in some code to allow overlaying annotation and expression data - happy to contribute these mods as pull requests if you want them. Our installation is private for now, but we'll make transition to public as relevant papers come out.

[Yannick Wurm]

Thanks Richard :) Pull requests are extremely welcome! Cheers!

[farman]

My existing custom databases are not showing up as blastable options in the web interface. I tried pointing to my existing blast database folder (blastDB) in the config file, as well as new folder that I created (blast_databases), in case the executable required a specific folder name.

[Yannick Wurm]

Hi @farman - sorry you've struggled with this & apologies I didn't see your message earlier. I hope you found some help on the sequenceserver mailing list accessible from http://sequenceserver.com

Answer 1

[Yannick Wurm]

Quick heads up that we recently released a new update resulting from a complete rewrite. It includes:

• graphcial overview
• flexible downloading
• guided configuration (e.g. downloads BLAST binaries if needed)
• beautiful user interface (much better than before)

Accessible at http://sequenceserver.com

Answer 2

[Yannick Wurm]

There have been a bunch of revisions/improvements since those posts. My writing today is to announce our pre-publication manuscript:

Biorxiv: http://dx.doi.org/10.1101/033142

Sequenceserver: a modern graphical user interface for custom BLAST databases

Anurag Priyam, Ben J Woodcroft, Vivek Rai, Alekhya Munagala, Ismail Moghul, Filip Ter, Mark Anthony Gibbins, HongKee Moon, Guy Leonard, Wolfgang Rumpf, Yannick Wurm

Importantly, the manuscript includes many details regarding the philosophy and software engineering approaches used for this project.