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, 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.
Installation & configuration
Linux or Mac and Ruby (≥ 1.8.7; preferably ≥ 2.0). Additionally, the
ruby-devpackage on Ubuntu and Debian.
NCBI BLAST+ (2.2.31+) is interactively downloaded if absent.
or or 7+ or 9+
Run the following in a terminal to install SequenceServer for the first time, or to update to the latest version:
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!
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
License & support
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.
Users & citations
- 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.
- Lamb et al. (2018) Evolution of the shut-off steps of vertebrate phototransduction. Open Biology.
- Elsik et al. (2018) Hymenoptera Genome Database: Using HymenopteraMine to enhance genomic studies of hymenopteran insects. Eukaryotic Genomic Databases, Methods in Molecular Biology.
- Hagen et al. (2018) Bovine Genome Database: Tools for mining the Bos taurus genome. Eukaryotic Genomic Databases, Methods in Molecular Biology.
- Blanchoud et al. (2018) De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. Scientific Reports.
- Naas et al. (2017) Beta-lactamase database (BLDB) – structure and function Journal of Enzyme Inhibition and Medicinal Chemistry.
- Seim et al. (2017) Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines. G3: Genes, Genomes, Genetics.
- Pracana et al. (2017) Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins. Evolution Letters.
- Borrell et al. (2017) Ecological Genomics for the Conservation of Dwarf Birch. PhD thesis.
- Suwansa-ard et al. (2017) Transcriptomic discovery and comparative analysis of neuropeptide precursors in sea cucumbers (Holothuroidea). Peptides.
- McCormick et al. (2017) High-Throughput Genotyping Analyses and Image-based Phenotyping in Sorghum bicolor. Diss.
- Carson et al. (2017) Bacteriocins of non-aureus staphylococci isolated from bovine milk. Applied and Environmental Microbiology.
- 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.
- Hill et al. (2017) HopBase: a unified resource for Humulus genomics. Database.
- Torres et al. (2017) LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. Database.
- Zhu et al. (2017) CottonFGD: an integrated functional genomics database for cotton. BMC Plant Biology.
- 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
- McCormick et al. (2016) 3D sorghum reconstructions from depth images enable identification of quantitative trait loci regulating shoot architecture. bioRxiv
- Liew et al. (2016) Reefgenomics.Org - a repository for marine genomics data. Database.
- Louro et al. (2016) Having a BLAST: Searchable transcriptome resources for the gilthead sea bream and the European sea bass. Marine Genomics.
- Torrens-Spence et al. (2016) A Workflow for Studying Specialized Metabolism in Nonmodel Eukaryotic Organisms. Methods in Enzymology.
- Nakagawa et al. (2016) gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. Database.
- Challis et al. (2016) Lepbase: the Lepidopteran genome database. bioRxiv.
- 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.
- Fu et al. (2016) Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq. Biotechnology for Biofuels.
- Semmens et al. (2016) Transcriptomic identification of starfish neuropeptide precursors yields new insights into neuropeptide evolution. Open Biology.
- Page et al. (2016) blastjs: a BLAST+ wrapper for Node.js. BMC Research Notes.
- Seim et al. (2016) Multi-species sequence comparison reveals conservation of ghrelin gene-derived splice variants encoding a truncated ghrelin peptide. Endocrine.
- Janies et al. (2016) EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC Bioinformatics.
- 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.
- Castro et al. (2015) Identification and heterologous expression of the chaxamycin biosynthesis gene cluster from Streptomyces leeuwenhoekii. Applied and Environmental Microbiology.
- Semmens et al. (2015) Discovery of sea urchin NGFFFamide receptor unites a bilaterian neuropeptide family. Open Biology.
- Petrillo et al. (2015) JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms. Database.
- 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.
- Kirmitzoglou I (2015) LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences. Bioinformatics.
- Elphick MR (2015) Reconstructing SALMFamide neuropeptide precursor evolution in the phylum Echinodermata: ophiuroid and crinoid sequence data provide new insights. Frontiers in Endocrinology.
- 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.
- Rodrigues M (2014) Molecular biology approaches in bioadhesion research. Beilstein Journal of Nanotechnology.
- Sharma P (2014) WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing. PLoS ONE.
- Mondav R et al. (2014) Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications.
- 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.
- 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.
- Chiu JC et al. (2013) Genome of Drosophila suzukii, the Spotted Wing Drosophila. G3.
- 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.
- Berlamino et al. (2013) SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis. BMC Bioinformatics.
- 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.
- Pathogen-Host Interactions database.
- Reef Genomics.
- Max Planck Institute for Developmental Biology. Pristionchus (animal).
- Max Planck Institute of Molecular Cell Biology and Genetics. Planarians (animal).
- Michigan State University. Electric fish (animal).
- New York University. Flies (animal).
- Oregon State University. Drosophila suzukii (animal).
- Peking University. Macaca mulatta (animal).
- Universita degli Studi di Milano. Streptocarpus rexii.
- University of Athens. Fungal mitochondria.
- University of Cambridge. Protists.
- University of Cyprus. UniProt.
- University of Exeter. Blastocladiella emersonii.
- University of Maryland. Astyanax (animal).
- BioCloud.ca (flounder) (animal).
- Dr. Wolfang Rumpf @ U Maryland.
- Spotted Drosophila Flybase @ Oregon State.
- Amborella Genome at University of Georgia.
- Jekely Lab at Max Planck Institute for Developmental Biology, Tübingen.
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.