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:

Sequenceserver: a modern graphical user interface for custom BLAST databases. Molecular Biology and Evolution (2019).
  • 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)

  • NCBI BLAST+ (2.2.31+) is interactively downloaded if absent

  • One of SequenceServer's dependencies (the module used to parse BLAST's XML output) compiles some C code as part of the installation process. This means that the standard Unix build tools (e.g., gcc, make) are required to install SequenceServer. 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 ruby-dev and build-essential packages in addition to ruby.

Once you have Ruby and the build tools installed, the command below can be used to install SequenceServer. Later on, the same command can be used to update SequenceServer to the latest version:

sudo gem install sequenceserver

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:


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

Please cite

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 actively develop and advance 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: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.

In addition to the research conducted and resources created using SequenceServer (below), several users have written articles about installing and customising SequenceServer:

  1. Zhang (2020) NBIGV-DB: a dedicated database of non-B cell derived immunoglobulin variable region. Gene.
  2. Swann (2020) The immunogenetics of sexual parasitism. Science.
  3. Colin (2020) The chloroalkaloid (−)-acutumine is biosynthesized via a Fe(II)- and 2-oxoglutarate-dependent halogenase in Menispermaceae plants. Nature Communications.
  4. Li (2020) Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis. Genome Research.
  5. Yañez-Guerra (2020) Echinoderms provide missing link in the evolution of PrRP/sNPF-type neuropeptide signalling. eLife.
  6. Hart (2020) Visual Opsin Diversity in Sharks and Rays. Molecular Biology and Evolution.
  7. Gauthier (2020) Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone. Molecular Ecology.
  8. Dallinger (2020) Metallomics reveals a persisting impact of cadmium on the evolution of metal-selective snail metallothioneins. Metallomics.
  9. Koch (2020) Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii. Scientific Reports.
  10. Gui (2020) ZEAMAP, a Comprehensive Database Adapted to the Maize Multi-Omics Era. iScience.
  11. Wu (2020) PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants. Database.
  12. Moreland (2020) The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. Database.
  13. Yu (2020) SAGER: a database of Symbiodiniaceae and Algal Genomic Resource. Database.
  14. Reichler (2020) Interventions designed to control postpasteurization contamination in high-temperature, short-time-pasteurized fluid milk processing facilities: A case study on the effect of employee training, clean-in-place chemical modification, and preventive maintenance programs. Journal of Dairy Science.
  15. Wang (2020) Coexpression Analysis Reveals Dynamic Modules Regulating the Growth and Development of Cirri in the Rattans (Calamus simplicifolius and Daemonorops jenkinsiana). Frontiers in Genetics.
  16. Triant (2020) Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. Animal Genetics.
  17. Goodheart (2020) Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): Developing a model system for the evolution of marine bioluminescence. Scientific Reports.
  18. Waterhouse (2020) Characterization of Insect Immune Systems from Genomic Data. Immunity in Insects. Springer Protocols Handbooks.
  19. Singh (2020) Overview of Genomic Resources Available for Lupins with a Focus on Narrow-Leafed Lupin (Lupinus angustifolius). The Lupin Genome. Compendium of Plant Genomes. Springer, Cham.
  20. Alves (2020) Incorporating personality in user interface design: A review. Personality and Individual Differences.
  21. Wang et al. (2020) MaGenDB: a functional genomics hub for Malvaceae plants. bioRxiv.
  22. Shamimuzzaman et al. (2020) Bovine Genome Database: new annotation tools for a new reference genome. Nucleic Acids Research.
  23. Almansoura and Alhagrib (2019) MMRdb: Measles, mumps, and rubella viruses database and analysis resource. Infection, Genetics and Evolution.
  24. Li et al. (2019) Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus. Genome Biology and Evolution.
  25. Bublitz et al. (2019) Peptidoglycan Production by an Insect-Bacterial Mosaic. Cell.
  26. Prieto et al. (2019) Grape Biotechnology: Past, Present, and Future. SpringerLink.
  27. Barbosa et al. (2019) ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp. PLoS Neglected Tropical Disease.
  28. Ravindran et al. (2019) Daphnia stressor database: Taking advantage of a decade of Daphnia ‘-omics’ data for gene annotation. Scientific Reports.
  29. Mirdita et al. (2019) MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics.
  30. Li et al. (2019) First mitochondrial genome of a periwinkle from the genus Littoraria: Littoraria sinensis. Mitochondrial DNA Part B
  31. Chen et al. (2019) Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis. Scientific Reports.
  32. Wagner et al. (2019) The ectomycorrhizospheric habitat of Norway spruce and Tricholoma vaccinum: Promotion of plant growth and fitness by a rich microorganismic community. Frontiers in Microbiology.
  33. Rungrat et al. (2019) A genome-wide association study of non-photochemical quenching in response to local seasonal climates in Arabidopsis thaliana. Plant Direct.
  34. Bizzarri et al. (2019) Interplay of chimeric mating-type loci impairs fertility rescue and accounts for intra-strain variability in Zygosaccharomyces rouxii interspecies hybrid ATCC42981. Frontiers in Genetics.
  35. Nowicki et al. (2019) Taraxacum kok-saghyz (rubber dandelion) genomic microsatellite loci reveal modest genetic diversity and cross-amplify broadly to related species. Scientific Reports.
  36. Liang et al. (2019) Developmental expression and evolution of hexamerin and haemocyanin from Folsomia candida (Collembola). Insect Molecular Biology.
  37. Meng et al. (2019) CircFunBase: a database for functional circular RNAs. Database.
  38. Moghul et al. (2019) Choosing the best gene predictions with GeneValidator. Kollmar M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962.
  39. Brandies et al. (2018) Disentangling the mechanisms of mate choice in a captive koala population. PeerJ.
  40. Young et al. (2018) Evidence for sexual reproduction: Identification, frequency, and spatial distribution of Venturia effusa (pecan scab) mating type idiomorphs Ecology and Epidemiology.
  41. Reichler et al. (2018) Pseudomonas fluorescens group bacterial strains are responsible for repeat and sporadic postpasteurization contamination and reduced fluid milk shelf life Journal of Dairy Science.
  42. Torrens-Spence et al. (2018) Complete pathway elucidation and heterologous reconstitution of Rhodiola salidroside biosynthesis. Molecular Plant.
  43. Lamb et al. (2018) Evolution of the shut-off steps of vertebrate phototransduction. Open Biology.
  44. Elsik et al. (2018) Hymenoptera Genome Database: Using HymenopteraMine to enhance genomic studies of hymenopteran insects. Eukaryotic Genomic Databases, Methods in Molecular Biology.
  45. Hagen et al. (2018) Bovine Genome Database: Tools for mining the Bos taurus genome. Eukaryotic Genomic Databases, Methods in Molecular Biology.
  46. Blanchoud et al. (2018) De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. Scientific Reports.
  47. Fallon et al. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife.
  48. Sanders et al. (2018) FusoPortal: An interactive repository of hybrid MinION-sequenced Fusobacterium genomes improves gene identification and characterization. mSphere.
  49. Dvorak et al. (2018) Metal binding functions of metallothioneins in the slug Arion vulgaris differ from metal-specific isoforms of terrestrial snails. Metallomics.
  50. Chen et al. (2018) MGH: a genome hub for the medicinal plant maca (Lepidium meyenii). Database.
  51. Borrell et al. (2018) Genetic diversity maintained among fragmented populations of a tree undergoing range contraction. Heredity.
  52. Torrens-Spence et al. (2018) Monoamine biosynthesis via a noncanonical calcium-activatable aromatic amino acid decarboxylase in psilocybin mushroom. ACS Chemical Biology.
  53. Tangherlini et al. (2018) GLOSSary: The global ocean 16S subunit web accessible resource BMC Bioinformatics.
  54. Challis et al. (2017) GenomeHubs: Simple containerized setup of a custom Ensembl database and web server for any species. Database.
  55. Kim et al. (2017) The genome of the freshwater monogonont rotifer Brachionus calyciflorus. Molecular Ecology Resources
  56. Naas et al. (2017) Beta-lactamase database (BLDB) – structure and function Journal of Enzyme Inhibition and Medicinal Chemistry.
  57. Seim et al. (2017) Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines. G3: Genes, Genomes, Genetics.
  58. Pracana et al. (2017) Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins. Evolution Letters.
  59. Suwansa-ard et al. (2017) Transcriptomic discovery and comparative analysis of neuropeptide precursors in sea cucumbers (Holothuroidea). Peptides.
  60. Carson et al. (2017) Bacteriocins of non-aureus staphylococci isolated from bovine milk. Applied and Environmental Microbiology.
  61. Shockey et al. (2017) Naturally occurring high oleic acid cottonseed oil: identification and functional analysis of a mutant allele of Gossypium barbadense fatty acid desaturase-2. Planta.
  62. Hill et al. (2017) HopBase: a unified resource for Humulus genomics. Database.
  63. Torres et al. (2017) LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. Database.
  64. Zhu et al. (2017) CottonFGD: An integrated functional genomics database for cotton. BMC Plant Biology.
  65. Wang et al. (2017) QTL mapping of selenium content using a RIL population in wheat BMC Plant Biology.
  66. Urban et al. (2016) PHI-base: A new interface and further additions for the multi-species pathogen–host interactions database Scientific Reports.
  67. Mun et al. (2016) Lotus Base: An integrated information portal for the model legume Lotus japonicus. Scientific Reports.
  68. Shen et al. (2016) Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3: Genes, Genomes, Genetics
  69. McCormick et al. (2016) 3D sorghum reconstructions from depth images enable identification of quantitative trait loci regulating shoot architecture. bioRxiv
  70. Liew et al. (2016) Reefgenomics.Org - a repository for marine genomics data. Database.
  71. Louro et al. (2016) Having a BLAST: Searchable transcriptome resources for the gilthead sea bream and the European sea bass. Marine Genomics.
  72. Torrens-Spence et al. (2016) A Workflow for Studying Specialized Metabolism in Nonmodel Eukaryotic Organisms. Methods in Enzymology.
  73. Nakagawa et al. (2016) gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. Database.
  74. Challis et al. (2016) Lepbase: the Lepidopteran genome database. bioRxiv.
  75. Hane et al. (2016) A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: Insights into plant‐microbe interactions and legume evolution. Plant Biotechnology Journal.
  76. Fu et al. (2016) Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq. Biotechnology for Biofuels.
  77. Semmens et al. (2016) Transcriptomic identification of starfish neuropeptide precursors yields new insights into neuropeptide evolution. Open Biology.
  78. Page et al. (2016) blastjs: a BLAST+ wrapper for Node.js. BMC Research Notes.
  79. Seim et al. (2016) Multi-species sequence comparison reveals conservation of ghrelin gene-derived splice variants encoding a truncated ghrelin peptide. Endocrine.
  80. Janies et al. (2016) EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC Bioinformatics.
  81. Bernonville, Foureau, Parage et al. (2015) Characterization of a second secologanin synthase isoform producing both secologanin and secoxyloganin allows enhanced de novo assembly of a Catharanthus roseus transcriptome. BMC Genomics.
  82. Castro et al. (2015) Identification and heterologous expression of the chaxamycin biosynthesis gene cluster from Streptomyces leeuwenhoekii. Applied and Environmental Microbiology.
  83. Semmens et al. (2015) Discovery of sea urchin NGFFFamide receptor unites a bilaterian neuropeptide family. Open Biology.
  84. Petrillo et al. (2015) JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms. Database.
  85. Seim et al. (2015) Comparative analysis reveals loss of the appetite-regulating peptide hormone ghrelin in falcons. General and Comparative Endocrinology.
  86. Elsik et al. (2015) Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. Nucleic Acids Research.
  87. Brandl et al. (2015) PlanMine – a mineable resource of planarian biology and biodiversity. Nucleic Acids Research.
  88. Kirmitzoglou I (2015) LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences. Bioinformatics.
  89. Elphick MR (2015) Reconstructing SALMFamide neuropeptide precursor evolution in the phylum Echinodermata: ophiuroid and crinoid sequence data provide new insights. Frontiers in Endocrinology.
  90. Gupta Y et al. (2015) De novo assembly and characterization of transcriptomes of early-stage fruit from two genotypes of Annona squamosa L. with contrast in seed number. BMC Genomics.
  91. Rodrigues M (2014) Molecular biology approaches in bioadhesion research. Beilstein Journal of Nanotechnology.
  92. Sharma P (2014) WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing. PLoS ONE.
  93. Mondav R et al. (2014) Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications.
  94. Rowe ML et al. (2014) Neuropeptides and polypeptide hormones in echinoderms: New insights from analysis of the transcriptome of the sea cucumber Apostichopus japonicus. General and Comparative Endocrinology.
  95. Chiara M et al. (2013) De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters. PLoS ONE.
  96. Semmens DC et al. (2013) Discovery of a novel neurophysin-associated neuropeptide that triggers cardiac stomach contraction and retraction in starfish. Journal of Experimental Biology.
  97. Chiu JC et al. (2013) Genome of Drosophila suzukii, the Spotted Wing Drosophila. G3.
  98. Shreve J et al. (2013) A genome-wide survey of small interfering RNA and microRNA pathway genes in a galling insect. Journal of Insect Physiology.
  99. Berlamino et al. (2013) SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis. BMC Bioinformatics.
  100. Elphick MR et al. (2013) The evolution and diversity of SALMFamide neuropeptides. PLoS ONE.
  101. Elphick MR (2012) The protein precursors of peptides that affect the mechanics of connective tissue and/or muscle in the echinoderm Apostichopus japonicus. PLoS ONE.
  1. Exome of Kronos durum wheat and Cadenza bread wheat mutants. John Innes Centre; Earlham Institute; HHMI; Rothamsted Research.
  2. Gene expression analysis and visualisation for wheat. John Innes Centre; Earlham Institute; BBSRC; IWYP; DFW.
  3. Beta-Lactamase DataBase (BLDB). JPIAMR transnational project DesInMBL; Région Ile-de-France (DIM Malinf); Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT).
  4. PC3 and LNCaP Human Prostate Cancer Cell Lines. GhrelinLab.
  5. NBIGV: Non-B cell dervied immunoglobulin variable region database. Peking University Health Science Center.
  6. Measles, mumps and rubella virsues database and analysis resource. Imam Abdulrahman Bin Faisal University.
  7. FusoPortal: A Fusobacterium genome and bioinformatic repository (pathogen). The Slade Lab, Virginia Tech.
  8. JRC GMO-Amplicons: database of sequences related to genetically modified organisms. Joint Research Centre, European Union Reference Laborator for GM Food and Feed.
  9. Pathogen-Host Interactions database (PHI-base). Rothamsted Research, UK.
  10. Cotton Functional Genomics Database (CottonFGD). Biotechnology Research Institute, Chinese Academy of Agricultural Sciences.
  11. Database for the model legume Lotus japonicus (Lotus Base). Centre for Carbohydrate Recognition and Signalling, Aarhus University.
  12. Cacao genome database. MARS; USDA/ARS; IBM; Clemson University Genomics Institute; PIPRA; HudsonAlpha Institute of Biotechnology; National Center for Genome Resources; Indiana University; Washington State University.
  13. Genome, predicted transcripts and proteins of tardigrades. Keio University; University of Edinburgh; BBSRC.
  14. Database of Tribolium RNAi phenotypes (iBeetle-Base). Georg-August-Universität Göttingen.
  15. Y1000+ project (yeast). University of Wisconsin-Madison; USDA; Vanderbilt University.
  16. MitoFun: A curated resource of complete fungal mitochondrial genomes. Bioinformatics Research Laboratory, University of Cyprus and Department of Genetics and Biotechnology, University of Athens
  17. Medaka Omics Data Portal. Tu Lab, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing.
  18. The Bovine Genome Database. University of Missouri.
  19. Spotted wing fly base (Drosophila suzukii), UC Davis and Oregon State University
  20. Lepidopteran genome database (Lepbase)
  21. Reef Genomics. King Abdullah University of Science and Technology.
  22. Echinoderms transcriptomes (EchinoDB). University of North Carolina at Charlotte.
  23. PlanMine (planarians), Max Planck Institute of Molecular Cell Biology and Genetics
  24. Firefly genome database
  25. MarpolBase: Genome database for the common liverwort, Marchantia polymorpha. Tohoku University.
  26. Oat genome. UNC Charlotte; Brigham Young University; Aberystwyth University.
  27. Crop genomics lab's BLAST server. Seoul National University.
  28. Asparagus genome project. University of Georgia.
  29. Narrow-leafed lupin genome project. Commonwealth Scientific and Industrial Research Organisation.
  30. Daphnia STRESSOR database. Universität Hamburg.
  31. Aplysia transcriptome, Institute for Genome Sciences, University of Maryland, Baltimore.
  32. HopBase (plant), Oregon State University
  33. Phalaenopsis aphrodite (plant) genome, transcripts, and proteins. Taiwan Agricultural Genomics Resource Center
  34. Hieracium (hawkweed). Commonwealth Scientific and Industrial Research Organisation.
  35. Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
  36. Stazione Zoologica Anton Dohrn
  37. Genome database for Iberian ribbed newt.
  38. Spiny mouse transcriptome
  39. Fish genome database
  40. Sea bass and sea bream transcripts, Dipartimento di Bioscienze, Università degli Studi di Milano
  41. Pristionchus (nematodes), Max Planck Institute for Developmental Biology.
  42. Electric fish, Michigan State University
  43. Flies (animal), New York University
  44. Streptocarpus rexii (plant), Universita degli Studi di Milano
  45. LCR-eXXXplorer, University of Cyprus
  46. The Richards' Lab (fungi, pseudofungi), University of Exeter
  47. The Amborella Genome (plant). University of Georgia.
  48. 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...