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:

sequenceserver

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. Chen et al. (2019) Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis. Scientific Reports.
  2. 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
  3. Rungrat et al. (2019) A genome-wide association study of non-photochemical quenching in response to local seasonal climates in Arabidopsis thaliana. Plant Direct.
  4. 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.
  5. 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.
  6. Liang et al. (2019) Developmental expression and evolution of hexamerin and haemocyanin from Folsomia candida (Collembola). Insect Molecular Biology.
  7. Meng et al. (2019) CircFunBase: a database for functional circular RNAs. Database.
  8. Moghul et al. (2019) Choosing the best gene predictions with GeneValidator. Kollmar M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962.
  9. Brandies et al. (2018) Disentangling the mechanisms of mate choice in a captive koala population. PeerJ.
  10. Young et al. (2018) Evidence for sexual reproduction: Identification, frequency, and spatial distribution of Venturia effusa (pecan scab) mating type idiomorphs Ecology and Epidemiology.
  11. 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.
  12. Torrens-Spence et al. (2018) Complete pathway elucidation and heterologous reconstitution of Rhodiola salidroside biosynthesis. Molecular Plant.
  13. Lamb et al. (2018) Evolution of the shut-off steps of vertebrate phototransduction. Open Biology.
  14. Elsik et al. (2018) Hymenoptera Genome Database: Using HymenopteraMine to enhance genomic studies of hymenopteran insects. Eukaryotic Genomic Databases, Methods in Molecular Biology.
  15. Hagen et al. (2018) Bovine Genome Database: Tools for mining the Bos taurus genome. Eukaryotic Genomic Databases, Methods in Molecular Biology.
  16. Blanchoud et al. (2018) De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. Scientific Reports.
  17. Fallon et al. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles eLife.
  18. Sanders et al. (2018) FusoPortal: An interactive repository of hybrid MinION-sequenced Fusobacterium genomes improves gene identification and characterization mSphere.
  19. Dvorak et al. (2018) Metal binding functions of metallothioneins in the slug Arion vulgaris differ from metal-specific isoforms of terrestrial snails. Metallomics.
  20. Chen et al. (2018) MGH: a genome hub for the medicinal plant maca (Lepidium meyenii). Database.
  21. Borrell et al. (2018) Genetic diversity maintained among fragmented populations of a tree undergoing range contraction. Heredity.
  22. Torrens-Spence et al. (2018) Monoamine biosynthesis via a noncanonical calcium-activatable aromatic amino acid decarboxylase in psilocybin mushroom. ACS Chemical Biology.
  23. Tangherlini et al. (2018) GLOSSary: The global ocean 16S subunit web accessible resource BMC Bioinformatics.
  24. Challis et al. (2017) GenomeHubs: Simple containerized setup of a custom Ensembl database and web server for any species. Database.
  25. Kim et al. (2017) The genome of the freshwater monogonont rotifer Brachionus calyciflorus. Molecular Ecology Resources
  26. Naas et al. (2017) Beta-lactamase database (BLDB) – structure and function Journal of Enzyme Inhibition and Medicinal Chemistry.
  27. Seim et al. (2017) Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines. G3: Genes, Genomes, Genetics.
  28. Pracana et al. (2017) Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins. Evolution Letters.
  29. Borrell et al. (2017) Ecological Genomics for the Conservation of Dwarf Birch. PhD thesis.
  30. Suwansa-ard et al. (2017) Transcriptomic discovery and comparative analysis of neuropeptide precursors in sea cucumbers (Holothuroidea). Peptides.
  31. McCormick et al. (2017) High-Throughput Genotyping Analyses and Image-based Phenotyping in Sorghum bicolor. Diss.
  32. Carson et al. (2017) Bacteriocins of non-aureus staphylococci isolated from bovine milk. Applied and Environmental Microbiology.
  33. 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.
  34. Hill et al. (2017) HopBase: a unified resource for Humulus genomics. Database.
  35. Torres et al. (2017) LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. Database.
  36. Zhu et al. (2017) CottonFGD: An integrated functional genomics database for cotton. BMC Plant Biology.
  37. Wang et al. (2017) QTL mapping of selenium content using a RIL population in wheat BMC Plant Biology.
  38. Urban et al. (2016) PHI-base: A new interface and further additions for the multi-species pathogen–host interactions database Scientific Reports.
  39. Mun et al. (2016) Lotus Base: An integrated information portal for the model legume Lotus japonicus. Scientific Reports.
  40. Shen et al. (2016) Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3: Genes, Genomes, Genetics
  41. McCormick et al. (2016) 3D sorghum reconstructions from depth images enable identification of quantitative trait loci regulating shoot architecture. bioRxiv
  42. Liew et al. (2016) Reefgenomics.Org - a repository for marine genomics data. Database.
  43. Louro et al. (2016) Having a BLAST: Searchable transcriptome resources for the gilthead sea bream and the European sea bass. Marine Genomics.
  44. Torrens-Spence et al. (2016) A Workflow for Studying Specialized Metabolism in Nonmodel Eukaryotic Organisms. Methods in Enzymology.
  45. Nakagawa et al. (2016) gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. Database.
  46. Challis et al. (2016) Lepbase: the Lepidopteran genome database. bioRxiv.
  47. 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.
  48. Fu et al. (2016) Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq. Biotechnology for Biofuels.
  49. Semmens et al. (2016) Transcriptomic identification of starfish neuropeptide precursors yields new insights into neuropeptide evolution. Open Biology.
  50. Page et al. (2016) blastjs: a BLAST+ wrapper for Node.js. BMC Research Notes.
  51. Seim et al. (2016) Multi-species sequence comparison reveals conservation of ghrelin gene-derived splice variants encoding a truncated ghrelin peptide. Endocrine.
  52. Janies et al. (2016) EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC Bioinformatics.
  53. 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.
  54. Castro et al. (2015) Identification and heterologous expression of the chaxamycin biosynthesis gene cluster from Streptomyces leeuwenhoekii. Applied and Environmental Microbiology.
  55. Semmens et al. (2015) Discovery of sea urchin NGFFFamide receptor unites a bilaterian neuropeptide family. Open Biology.
  56. Petrillo et al. (2015) JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms. Database.
  57. Seim et al. (2015) Comparative analysis reveals loss of the appetite-regulating peptide hormone ghrelin in falcons. General and Comparative Endocrinology.
  58. Elsik et al. (2015) Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. Nucleic Acids Research.
  59. Brandl et al. (2015) PlanMine – a mineable resource of planarian biology and biodiversity. Nucleic Acids Research.
  60. Kirmitzoglou I (2015) LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences. Bioinformatics.
  61. Elphick MR (2015) Reconstructing SALMFamide neuropeptide precursor evolution in the phylum Echinodermata: ophiuroid and crinoid sequence data provide new insights. Frontiers in Endocrinology.
  62. 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.
  63. Rodrigues M (2014) Molecular biology approaches in bioadhesion research. Beilstein Journal of Nanotechnology.
  64. Sharma P (2014) WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing. PLoS ONE.
  65. Mondav R et al. (2014) Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications.
  66. 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.
  67. 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.
  68. 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.
  69. Chiu JC et al. (2013) Genome of Drosophila suzukii, the Spotted Wing Drosophila. G3.
  70. 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.
  71. Berlamino et al. (2013) SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis. BMC Bioinformatics.
  72. Elphick MR et al. (2013) The evolution and diversity of SALMFamide neuropeptides. PLoS ONE.
  73. 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. MitoFun: A curated resource of complete fungal mitochondrial genomes, Bioinformatics Research Laboratory, University of Cyprus and Department of Genetics and Biotechnology, University of Athens
  2. Taiwan Agricultural Genomics Resource Center
  3. Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
  4. Commonwealth Scientific and Industrial Research Organisation
  5. Georgia State University
  6. Stazione Zoologica Anton Dohrn
  7. Fungal genomics, Microbiology lab, Utrecht University
  8. Gene expression analysis and visualisation for wheat
  9. Exome of Kronos durum wheat and Cadenza bread wheat mutants
  10. Crop genomics lab's BLAST server, Seoul National University
  11. Genome database for Iberian ribbed newt,
  12. Measles, mumps and rubella virsues database and analysis resource, Imam Abdulrahman Bin Faisal University
  13. Spiny mouse transcriptome
  14. Oat genome, UNC Charlotte, Brigham Young University, Aberystwyth University
  15. MarpolBase: Genome database for the common liverwort, Marchantia polymorpha, Tohoku University
  16. Fish genome database
  17. NCHU fish genome database
  18. FusoPortal: A Fusobacterium genome and bioinformatic repository, The Slade Lab, Virginia Tech
  19. eplant.org: Sequenced genomes of all plants to facilitate comparative genomic studies
  20. Genome, predicted transcripts and proteins of tardigrades
  21. Firefly genome database
  22. Asparagus genome project
  23. Aplysia transcriptome
  24. Cacao genome database
  25. NBIGV, Non-B cell dervied immunoglobulin variable region database, Peking University Health Science Center
  26. Database of Tribolium RNAi phenotypes (iBeetle-Base), Georg-August-Universität Göttingen
  27. Genome-based Endogenous Viral Element (gEVE) Database, Biomedical Informatics Laboratory, Tokai University School of Medicine
  28. Lotus Base (Lotus japonicus), Centre for Carbohydrate Recognition and Signalling, Aarhus University
  29. Cotton Functional Genomics Database (CottonFGD), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences
  30. LeishDB (protozoa), Universidad Mayor
  31. HopBase (plant), Oregon State University
  32. Beta-Lactamase DataBase (BLDB)
  33. The Bovine Genome Database, University of Missouri
  34. PC3 and LNCaP Human Prostate Cancer Cell Lines, GhrelinLab
  35. Y1000+ project (yeast), University of Wisconsin-Madison
  36. JRC GMO-Amplicons
  37. Annona squamosa genome and transcripts, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology (DBT), India
  38. Sea bass and sea bream transcripts, Dipartimento di Bioscienze, Università degli Studi di Milano
  39. Lepidopteran genome database (Lepbase)
  40. Narrow-leafed lupin genome project, Commonwealth Scientific and Industrial Research Organisation
  41. Echinoderms transcriptomes (EchinoDB), University of North Carolina at Charlotte
  42. Daphnia STRESSOR database.
  43. Pathogen-Host Interactions database (PHI-base), Rothamsted Research, UK
  44. Reef Genomics
  45. Pristionchus (nematodes), Max Planck Institute for Developmental Biology.
  46. PlanMine (planarians), Max Planck Institute of Molecular Cell Biology and Genetics
  47. Electric fish, Michigan State University
  48. Flies (animal), New York University
  49. Spotted wing fly base (Drosophila suzukii), UC Davis and Oregon State University
  50. RhesusBase (Rhesus macaque) , Institute of Molecular Medicine, Peking University
  51. Streptocarpus rexii (plant), Universita degli Studi di Milano
  52. LCRs eXXXplorer, University of Cyprus
  53. The Richards' Lab (fungi, pseudofungi), University of Exeter
  54. The Amborella Genome (plant), University of Georgia
  55. 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...