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Intuitive local web frontend for the BLAST bioinformatics tool
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yeban Merge remote-tracking branch 'tomas/links_update'
* tomas/links_update:
  Added Rfam ID links
  Better regexp for Pfam ID
  Minor fix
  Updated links with PFAM; search also title, not only ID

Signed-off-by: Anurag Priyam <>
Latest commit 019b50f Mar 3, 2019
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LICENSE Switch to GNU AGPL version 3. Feb 23, 2015
lib Added Rfam ID links Feb 18, 2019
spec Set WEBrick as the server for Capybara Jan 15, 2019
views Ensure cache is refreshed when user updates sequenceserver Apr 18, 2018
.csslintrc Update codeclimate. Oct 11, 2016
.eslintrc Update codeclimate. Oct 11, 2016
.gitignore Revise front-end and build architecture. Aug 29, 2015
.mailmap Add .mailmap to correctly aggregate commits from same authors. Feb 5, 2015
.rspec Rubocop! Feb 2, 2015
.travis.yml Try to improve Capybara test suite Jan 15, 2019
COPYRIGHT.txt Switch to GNU AGPL version 3. Feb 23, 2015
Rakefile Ruby 1.9 hash syntax issues solved Jul 24, 2018 Add Capybara headless testing framework Dec 22, 2014

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SequenceServer - BLAST searching made easy!

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for personal or group use. If you use SequenceServer, please cite our preprint:

Priyam A, Woodcroft BJ, Rai V, Munagala A, Moghul I, Ter F, Gibbins MA, Moon H, Leonard G, Rumpf W & Wurm Y. 2015. Sequenceserver: A modern graphical user interface for custom BLAST databases. biorxiv doi: 10.1101/033142.

Install and configure

To install the old, stable version - 1.0.11 - please see

To get the latest 1.1.0-beta release, run:

gem install --pre sequenceserver

Version 1.1.0-beta releases are announced on Google Group. Summary of changes can also be viewed on our GitHub release page.

Develop and contribute

You will need Ruby and RubyGems, Node and npm, and CodeClimate.


Get source code and install dependencies.

git clone
gem install bundler
cd sequenceserver
npm install

If you just want to install and use SequenceServer from source you can skip npm install step, and skip installing gems used for testing:

git clone
gem install bundler
cd sequenceserver
bundle install --without=development

Run, test, build

Launch SequenceServer in development mode. In development mode SequenceServer logs verbosely and uses raw front-end files.

bundle exec bin/sequenceserver -D

Run tests:

bundle exec rspec

Run code style checkers (rubocop, csslint, eslint) -

codeclimate analyze

Build minifies JS and CSS bundles:

npm run-script build

Using Docker

# With database fasta files inside a folder named db
docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver


Big Thanks

Cross-browser Testing Platform and Open Source <3 Provided by Sauce Labs

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