Rapidly set up a BLAST+ server for yourself or for sharing datasets with your colleagues and your community. Focus on the biology: effectively and interpret BLAST with helpful visualizations.
SequenceServer is free and open source: install it yourself to run it on your personal computer, a departmental server.
Our SequenceServer Cloud service enables your team to run BLAST analyses in the cloud and provides a graphical interface for easy configuration and access management.
SequenceServer is extensively used in private and public sector labs for cloning, comparative genomics, gene curation, design of diagnostic markers and many other applications. Our software has helped research on humans, viruses, bacteria, agricultural plants and animals, and dozens of emerging model organisms. SequenceServer is a main querying mechanism for dozens of community databases (e.g., Drosophila suzukii, planarians, Lotus japonicus, echinoderms, ants, butterfly), and is also used for teaching.
Our highly cited 2019 MBE paper provides an overview of SequenceServer's user-centric design and sustainable software development philosophy.
Screenshot: BLAST result overview
Screenshot: Circos-style visualisation of BLAST queries and hits.
Screenshot: Length distribution of BLAST hits showing that the query (a predicted gene product) is longer than database hits sequences.
Screenshot: Pairwise BLAST alignment (Kablammo) visualization showing a translocated sequence.
Screenshot: BLAST search submission web interface
make) are required to install SequenceServer. This is because SequenceServer's need to parse BLAST's XML output compiles some C code as part of the installation process. This means that the On a Mac, this means having Xcode and CLI tools for Xcode installed. On Ubuntu and other Debian-based Linux systems, you would have to install the
build-essentialpackages in addition to
Once you have Ruby and the build tools installed, or Docker, the commands below can be used to install SequenceServer for the first time. Later on, the same command can be used to update SequenceServer to the latest version:
If using Docker:
Run the following in a terminal to configure and run SequenceServer. It will automatically download NCBI BLAST+ if absent, ask for the location of directory containing database sequences, format FASTA files for use with BLAST+, and list them for use in the search form:
If using Docker, you need to provide the databases directory up-front:
docker run -itp 4567:4567 -v /path-to-database-dir:/db wurmlab/sequenceserver
That's it! Open http://localhost:4567 in your web-browser and start BLAST-ing!
Installing SequenceServer is straightforward on most UNIX systems. However, this isn't for everyone.
Having spent 15 years running BLAST servers, we have now created SequenceServer Cloud. A hassle-free, secure and cost-effective solution for labs, institutions and individuals. Find out more.
SequenceServer is free to use by any individual or organization for all purposes under GNU AGPL version 3. Please see Razuna's licensing information page if in doubt. Our licensing model is same as theirs.
Sequenceserver: a modern graphical user interface for custom BLAST databases. Molecular Biology and Evolution (2019).
We request you to not remove the please cite line from your installation of SequenceServer. Citations are important for us to maintain and improve SequenceServer.
Have an issue in deploying SequenceServer? Something is not working as expected? Have a tip? A feature request? A Question about BLAST? Post to the SequenceServer BLAST Community Support Forum .
Customers of the SequenceServer Cloud BLAST service have dedicated support streams.
We are also available for consulting which can range from custom support to server deployment and administration to implementing specific features. Get in touch.
In addition to the research conducted and resources created using SequenceServer (below), several users have written articles about installing and customising SequenceServer:
Scholar is typically the best place to find the most recent citations. But we also have an outdated list here:
and many additional private installations that we don't know about...