SequenceServer lets you rapidly set up a BLAST+ server for individual use or for sharing datasets with colleagues and community. Its minimalist, modern and thoughtful design lets you focus on the Biology and getting things done. SequenceServer is free and open source.

SequenceServer has been used for research on emerging model organisms (e.g., sea cucumber, starfish, falcons, Hessian fly, sugar-apple tree, Streptocarpus rexii), and for research in bioadhesion and environmental microbiology. SequenceServer is a main querying mechanism for several community databases (e.g., Drosophila suzukii, planarians, birch and ash tree, Amborella, echinoderms, Fusarium, ants, butterfly), and is also used as an educational resource .

Read about SequenceServer's user-centric design and sustainable software development philosophy:

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.
  • Automatic detection of BLAST software - if absent the correct version is automatically downloaded.
  • Detects existing BLAST databases and automatically lists them in the search interface.
  • Detects sequence type of FASTA files and prompts to turn them into BLAST databases.
  • Built-in web server for light to medium usage. Can be integrated with Apache / Nginx if required.
  • Easily add custom links to search hits (e.g. to a genome browser or a page describing the sequence).
  • Type or paste query sequences, or drag-and-drop a FASTA file to search.
  • Smart user interface automagically figures out the appropriate BLAST method for the given query and selected databases.
  • Use advanced parameters as you would in the command line: -evalue 1.0e-10 -max_target_seqs 10
  • Graphical overview of results naturally separates strong from weak hits (by evalue).
  • GenBank style visualisation of hit sequences - residues grouped in multiples of five.
  • Download hit sequences in FASTA format, and alignment data in tab-delimited and XML format for further analysis.
  • Step-by-step discovery of workflow and options through interactive, visual feedback.
Screenshot of search interface.

Screenshot: Search interface


Screenshot of result interface.

Screenshot: Result interface


Setup process.

Screenshot: Setup process

  • Linux or Mac OSX. While we would like to also support Windows, our resources are limited and we prefer to first concentrate on making SequenceServer great on fewer platforms. It should be possible to run SequenceServer on Windows using Cygwin. Note that you can connect to SequenceServer running on other machines from your browser in Windows.

  • Ruby (≥ 1.8.7) along with the ruby-dev package on Darwin/Debian. NCBI BLAST+ (≥ 2.2.30+) is interactively downloaded if absent.

  • Google Chrome or Mozilla Firefox or Safari 7+ or Internet Explorer 9+

Run the following in a terminal to install, configure and run the latest release of SequenceServer. It will automatically guide you through an interactive setup process to locate or download BLAST+ binaries, ask for the location of FASTA files (or BLAST+ databases), and offer to create BLAST+ databases from FASTA files.

# Install or update.
sudo gem install sequenceserver

# Configure and run.
sequenceserver

Alternatively, you can use SequenceServer with Docker - only need to specify the location of your database directory.

docker run --rm -itp 4567:4567 -v /path-to-database-dir:/db wurmlab/sequenceserver

That's it! Open http://localhost:4567/ and start BLAST-ing!


Please cite

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.

We request you to not remove the please cite line from your installation of SequenceServer. Citations are important for us to actively develop and advance SequenceServer.

We have expanded, updated, and improved our documentation and moved it to the new advanced setup page.

SequenceServer is free to use by any individual or organization for all purposes under GNU AGPL version 3. Custom licensing is also possible if AGPL doesn't suit your needs - get in touch. Please see Razuna's licensing information page if in doubt. Our licensing model is same as theirs.

Have an issue in deploying SequenceServer? Something is not working as expected? Have a tip? A feature request? Or just want to encourage further development? Post it to SequenceServer Google Group and we will work something out. We are also available for consulting which can range from custom support to server deployment and administration to implementing specific features. Get in touch.

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Anurag Priyam is the lead developer and maintainer of the SequenceServer project. He is a research assistant at Dr. Wurm's Lab, Queen Mary University of London using a mix of new and established technologies to develop bioinformatics software to aid the study of emerging model organisms (e.g., crowdsourcing manual curation, virtual environment for bioinformatics analyses, genevalidator, annotation liftover).
Ben J Woodcroft is researching microbial responses to permafrost thaw (climate change induced), and the bioinformatics of metagenomics. He is a post-doctoral fellow at the Australia Centre for Ecogenomics.
Vivek Rai is an undergraduate student in Department of Biotechnology at Indian Institute Of Technology, Kharagpur. Besides programming, he is fascinated by Proteins, Computational Biology, and Bioinformatics.
Alekhya Munagala is a Math and Computing undergrad at the Indian Institute Of Technology, Kharagpur.
Ismail Moghul is Bioinformatics post-graduate at Queen Mary University of London.
Filip Ter is a Computer Science undergrad at Queen Mary University of London. He is interested in web technology, software development and exploring various programming methodologies.
Bruno Vieira is a PhD student in Bioinformatics at Dr. Wurm's Lab, Queen Mary University of London. He is the founder of the bionode project and a member of the Dat and oswitch team.
Mark Anthony Gibbins holds a Computer Science degree from Royal Holloway, University of London with a focus on Bioinformatics, and is currently a professional software engineer in the private sector. His interests in Bioinformatics are new alignment algorithms and building tools to improve research methods.
HongKee Moon is a Software Engineer at Scientific Computing Facility at Max Planck Institute of Molecular Cell Biology and Genetics. He is interested in software usability and visualization of scientific data.
Guy Leonard is a bioinformatician and works with comparative genomics, phylogenomics and genome assembly with an interest in the evolutionary relationships of eukaryotes and the cellular and genomic innovations of the diversity of eukaryotic cells.
Wolfgang Rumpf is a computational biologist at the Research Institute at Nationwide Children's Hospital, where he works towards creating better analytical devices and techniques to help diagnose and treat diseases.
Yannick Wurm is an evolutionary biologist using genomics tools to study the evolution of social insect societies (eg: antgenomes.org, fire ant genome, competing fire ant queens). He is a Senior Lecturer in Bioinformatics at Queen Mary University London.
Hiten Chowdhary is a Mathematics and Computing undergrad at the Indian Institute Of Technology, Kharagpur. He is a Google Summer of Code 2016 student, working on SequenceServer, building a Visualization tool for BLAST results.
Maybe you? The SequenceServer team will happily accept contributions. Please get in touch to figure out where you could fit in. Cheers!