SequenceServer lets you rapidly set up a BLAST+ server for individual use or for sharing datasets with your colleagues and your 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, falcon, 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.
  • Automatically detects 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 and Ruby (≥ 1.8.7; preferably ≥ 2.0). Additionally, the ruby-dev package on Ubuntu and Debian.

  • NCBI BLAST+ (2.2.31+) 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 SequenceServer for the first time, or to update to the latest version:

sudo gem install sequenceserver

Run the following in a terminal to configure and run SequenceServer. It will automatically prompt you for anything that might be missing:


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.

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:1.0.11

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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  1. Database of Tribolium RNAi phenotypes (iBeetle-Base), Georg-August-Universität Göttingen
  2. Genome-based Endogenous Viral Element (gEVE) Database, Biomedical Informatics Laboratory, Tokai University School of Medicine
  3. Lotus Base (Lotus japonicus), Centre for Carbohydrate Recognition and Signalling, Aarhus University
  4. Cotton Functional Genomics Database (CottonFGD), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences
  5. LeishDB (protozoa), Universidad Mayor
  6. HopBase (plant), Oregon State University
  7. Beta-Lactamase DataBase (BLDB)
  8. The Bovine Genome Database, University of Missouri
  9. PC3 and LNCaP Human Prostate Cancer Cell Lines, GhrelinLab
  10. Y1000+ project (yeast), University of Wisconsin-Madison
  11. JRC GMO-Amplicons
  12. Annona squamosa genome and transcripts, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology (DBT), India
  13. Sea bass and sea bream transcripts, Dipartimento di Bioscienze, Università degli Studi di Milano
  14. Lepidopteran genome database (Lepbase)
  15. Narrow-leafed lupin genome project, Commonwealth Scientific and Industrial Research Organisation
  16. Echinoderms transcriptomes (EchinoDB), University of North Carolina at Charlotte
  17. Daphnia STRESSOR database.
  18. Pathogen-Host Interactions database (PHI-base), Rothamsted Research, UK
  19. Reef Genomics
  20. Pristionchus (nematodes), Max Planck Institute for Developmental Biology.
  21. PlanMine (planarians), Max Planck Institute of Molecular Cell Biology and Genetics
  22. Electric fish, Michigan State University
  23. Flies (animal), New York University
  24. Spotted wing fly base (Drosophila suzukii), UC Davis and Oregon State University
  25. RhesusBase (Rhesus macaque) , Institute of Molecular Medicine, Peking University
  26. Streptocarpus rexii (plant), Universita degli Studi di Milano
  27. Fungal mitochondrial genomes, University of Athens
  28. LCRs eXXXplorer, University of Cyprus
  29. The Richards' Lab (fungi, pseudofungi), University of Exeter
  30. The Amborella Genome (plant), University of Georgia
  31. Jékely Lab (zooplanktons), Max Planck Institute for Developmental Biology, Tübingen

SequenceServer has satisfied users at U Melbourne, Centre for Organismal Studies Heidelberg, Swiss Institute of Bioinformatics, IIT Karagpur, Natural History Museum London, Queen Mary University London, Benaroya Research Institute, University of Lausanne

and many additional private installations that we don't know about...

SequenceServer was started by Dr. Yannick Wurm and Anurag Priyam to provide BLAST search for Fourmidable. And to fend off BLAST-search requests from colleagues: we wanted to point them to SequenceServer and say "it's so easy, you can do it yourself!" The team has grown ever since.

Anurag Priyam is pursuing PhD in genome bioinformatics at Dr. Yannick Wurm's Research Group, at Queen Mary University of London. [lab page]
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 a Biotechnology graduate from Indian Institute Of Technology, Kharagpur. He is currently a PhD Student with the Department of Computational Medicine and Bioinformatics at University of Michigan, Ann Arbor.
Alekhya Munagala is a Math and Computing undergrad at the Indian Institute Of Technology, Kharagpur.
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.
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.
Lawrence John Maynard is an undergraduate student of Genetics at Queen Mary University of London.
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 (e.g.:, fire ant genome, competing fire ant queens). He is a Senior Lecturer in Bioinformatics at Queen Mary University London.
Maybe you? The SequenceServer team will happily accept contributions. Please get in touch to figure out where you could fit in. Cheers!