SequenceServer BLAST search made easy!
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 and ash tree, Amborella, echinoderms, 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).
Easy to use
- 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.
- Several graphical overview of BLAST results help to understand the biology.
- 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.
Installing SequenceServer is straightforward on most UNIX systems (see below). However, this isn't for everyone.
- Perhaps you lack the infrastructure or would prefer a point-and-click setup.
- Or you want SequenceServer BLAST to run faster at a reasonable cost.
- Or want to be able to perform BLAST searches from anywhere, without having to worry about IPs, ports or power outages.
- Or you simply want to benefit from the greatest SequenceServer features without the hassle of running and updating a server.
Requirements for local installation
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.,
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
build-essentialpackages in addition to
Install or update
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:
Configure and run
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!
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.
Using with Docker
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:
- 2019: How to set up SequenceServer and Viroblast in Chinese!
- 2019: Part of a chapter in the book "Information technology for biological data analysis" (in Japanese!)
- 2018: SequenceServer: nice local blast by Bruno (installation on Centos 7.5)
- 2018: Post-mortem on downtime experienced by BLAST-related tools by Terry Mun (issues that may be encountered by community databases)
- 2018: How can I link BLAST results to JBrowse by JBrowse team (linking BLAST results with JBrowse genome browser)
- 2017: Tutorial for setting up SequenceServer and BLAST in Chinese!
- 2016: A video tutorial of SequenceServer in Japanese!
- 2015: Setting up SequenceServer by Terry Mun (shows the level of customisation that can be achieved with SequenceServer)
- 2015: Sequence Server by Zach Charlop-Powers (using SequenceServer on RedHat Linux)
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- Waterhouse (2020) Characterization of Insect Immune Systems from Genomic Data. Immunity in Insects. Springer Protocols Handbooks.
- Koch (2020) Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii. Scientific Reports.
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- Moreland (2020) The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. Database.
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- Barreira (2020) AniProtDB: A Collection of Uniformly Generated Metazoan Proteomes for Comparative Genomics Studies bioRxiv.
- Alves (2020) Incorporating personality in user interface design: A review. Personality and Individual Differences.
- Wang et al. (2020) MaGenDB: a functional genomics hub for Malvaceae plants. Nucleic Acids Research.
- Shamimuzzaman et al. (2020) Bovine Genome Database: new annotation tools for a new reference genome. Nucleic Acids Research.
- 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.
- Thole (2019) RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics. BMC Genomics.
- Prieto et al. (2019) Grape Biotechnology: Past, Present, and Future. SpringerLink.
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- Elsy (2019) Xenopus laevis FGF16 activates the expression of genes coding for the transcription factors Sp5 and Sp5l. International Journal of Developmental Biology.
- Li et al. (2019) Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus. Genome Biology and Evolution.
- Bublitz et al. (2019) Peptidoglycan Production by an Insect-Bacterial Mosaic. Cell.
- Lismont (2019) Using BRET-based G protein biosensors to unravel the G protein mediated pathways in insects. KU Leuven.
- Liou (2019) Enzyme structure, function, and evolution in flavonoid biosynthesis. Massachusetts Institute of Technology, Department of Biology.
- Botwright (2019) Greenlip Abalone (Haliotis laevigata) Genome and Protein Analysis Provides Insights into Maturation and Spawning. G3 Genes | Genomes | Genetics.
- Almansoura and Alhagrib (2019) MMRdb: Measles, mumps, and rubella viruses database and analysis resource. Infection, Genetics and Evolution.
- Barbosa et al. (2019) ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp. PLoS Neglected Tropical Disease.
- Levsh (2019) Independent evolution of rosmarinic acid biosynthesis in two sister families under the Lamiids clade of flowering plants. Journal of Biological Chemistry.
- Ravindran et al. (2019) Daphnia stressor database: Taking advantage of a decade of Daphnia ‘-omics’ data for gene annotation. Scientific Reports.
- Mirdita et al. (2019) MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics.
- Li et al. (2019) First mitochondrial genome of a periwinkle from the genus Littoraria: Littoraria sinensis. Mitochondrial DNA Part B
- Chen et al. (2019) Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis. Scientific Reports.
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- Rungrat et al. (2019) A genome-wide association study of non-photochemical quenching in response to local seasonal climates in Arabidopsis thaliana. Plant Direct.
- 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.
- 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.
- Liang et al. (2019) Developmental expression and evolution of hexamerin and haemocyanin from Folsomia candida (Collembola). Insect Molecular Biology.
- Meng et al. (2019) CircFunBase: a database for functional circular RNAs. Database.
- Moghul et al. (2019) Choosing the best gene predictions with GeneValidator. Kollmar M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962.
- Brandies et al. (2018) Disentangling the mechanisms of mate choice in a captive koala population. PeerJ.
- Young et al. (2018) Evidence for sexual reproduction: Identification, frequency, and spatial distribution of Venturia effusa (pecan scab) mating type idiomorphs Ecology and Epidemiology.
- 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.
- Torrens-Spence et al. (2018) Complete pathway elucidation and heterologous reconstitution of Rhodiola salidroside biosynthesis. Molecular Plant.
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- Hagen et al. (2018) Bovine Genome Database: Tools for mining the Bos taurus genome. Eukaryotic Genomic Databases, Methods in Molecular Biology.
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- Zhu et al. (2017) CottonFGD: An integrated functional genomics database for cotton. BMC Plant Biology.
- Wang et al. (2017) QTL mapping of selenium content using a RIL population in wheat BMC Plant Biology.
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- Mun et al. (2016) Lotus Base: An integrated information portal for the model legume Lotus japonicus. Scientific Reports.
- Shen et al. (2016) Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3: Genes, Genomes, Genetics
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- Semmens et al. (2016) Transcriptomic identification of starfish neuropeptide precursors yields new insights into neuropeptide evolution. Open Biology.
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- Seim et al. (2015) Comparative analysis reveals loss of the appetite-regulating peptide hormone ghrelin in falcons. General and Comparative Endocrinology.
- Elsik et al. (2015) Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. Nucleic Acids Research.
- Brandl et al. (2015) PlanMine – a mineable resource of planarian biology and biodiversity. Nucleic Acids Research.
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- 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.
- 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.
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- Elphick MR et al. (2013) The evolution and diversity of SALMFamide neuropeptides. PLoS ONE.
- 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.
- Exome of Kronos durum wheat and Cadenza bread wheat mutants. John Innes Centre; Earlham Institute; HHMI; Rothamsted Research.
- Gene expression analysis and visualisation for wheat. John Innes Centre; Earlham Institute; BBSRC; IWYP; DFW.
- 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).
- NBIGV: Non-B cell dervied immunoglobulin variable region database. Peking University Health Science Center.
- Measles, mumps and rubella virsues database and analysis resource. Imam Abdulrahman Bin Faisal University.
- FusoPortal: A Fusobacterium genome and bioinformatic repository (pathogen). The Slade Lab, Virginia Tech.
- JRC GMO-Amplicons: database of sequences related to genetically modified organisms. Joint Research Centre, European Union Reference Laborator for GM Food and Feed.
- Pathogen-Host Interactions database (PHI-base). Rothamsted Research, UK.
- Cotton Functional Genomics Database (CottonFGD). Biotechnology Research Institute, Chinese Academy of Agricultural Sciences.
- Database for the model legume Lotus japonicus (Lotus Base). Centre for Carbohydrate Recognition and Signalling, Aarhus University.
- 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.
- Genome, predicted transcripts and proteins of tardigrades. Keio University; University of Edinburgh; BBSRC.
- Database of Tribolium RNAi phenotypes (iBeetle-Base). Georg-August-Universität Göttingen.
- Y1000+ project (yeast). University of Wisconsin-Madison; USDA; Vanderbilt University.
- MitoFun: A curated resource of complete fungal mitochondrial genomes. Bioinformatics Research Laboratory, University of Cyprus and Department of Genetics and Biotechnology, University of Athens
- Medaka Omics Data Portal. Tu Lab, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing.
- The Bovine Genome Database. University of Missouri.
- Spotted wing fly base (Drosophila suzukii), UC Davis and Oregon State University
- Lepidopteran genome database (Lepbase)
- Reef Genomics. King Abdullah University of Science and Technology.
- Echinoderms transcriptomes (EchinoDB). University of North Carolina at Charlotte.
- PlanMine (planarians), Max Planck Institute of Molecular Cell Biology and Genetics
- Firefly genome database
- MarpolBase: Genome database for the common liverwort, Marchantia polymorpha. Tohoku University.
- Oat genome. UNC Charlotte; Brigham Young University; Aberystwyth University.
- Crop genomics lab's BLAST server. Seoul National University.
- Asparagus genome project. University of Georgia.
- Narrow-leafed lupin genome project. Commonwealth Scientific and Industrial Research Organisation.
- Daphnia STRESSOR database. Universität Hamburg.
- Aplysia transcriptome, Institute for Genome Sciences, University of Maryland, Baltimore.
- HopBase (plant), Oregon State University
- Phalaenopsis aphrodite (plant) genome, transcripts, and proteins. Taiwan Agricultural Genomics Resource Center
- Hieracium (hawkweed). Commonwealth Scientific and Industrial Research Organisation.
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
- Stazione Zoologica Anton Dohrn
- Genome database for Iberian ribbed newt.
- Spiny mouse transcriptome
- Fish genome database
- Sea bass and sea bream transcripts, Dipartimento di Bioscienze, Università degli Studi di Milano
- Electric fish, Michigan State University
- Flies (animal), New York University
- LCR-eXXXplorer, University of Cyprus
- The Amborella Genome (plant). University of Georgia.
and many additional private installations that we don't know about...