New article in the NAR Web Server Issue is now available
Our latest service update paper titled ‘The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024’ has been published in Nucleic Acids Research, Web Server Issue.
In this paper we update the community on the latest developments to Job Dispatcher. The abstract should give a good idea what Job Dispatcher is about and what the team has been up to in the last couple of years:
The EMBL-EBI Job Dispatcher sequence analysis tools framework (https://www.ebi.ac.uk/jdispatcher) enables the scientific community to perform a diverse range of sequence analyses using popular bioinformatics applications. Free access to the tools and required sequence datasets is provided through user-friendly web applications, as well as via RESTful and SOAP-based APIs. These are integrated into popular EMBL-EBI resources such as UniProt, InterPro, ENA and Ensembl Genomes. This paper overviews recent improvements to Job Dispatcher, including its brand new website and documentation, enhanced visualisations, improved job management, and a rising trend of user reliance on the service from low-and middle-income regions.
The main focus of the paper has been the new frontend application and documentation. The new JD website is available from https://www.ebi.ac.uk/jdispatcher, whereas the new documentation is available from https://www.ebi.ac.uk/jdispatcher/docs.
Utilizing a modern frontend framework, the website focuses on enhancing the user experience for both new and advanced users, with a particular emphasis on responsiveness and accessibility. Unlike the previous model, where pages were generated server-side in a monolithic application, the new design employs a separate frontend application that integrates seamlessly with the backend through JD’s REST API. This approach allows for greater flexibility in future development for both the frontend and the backend.
Key features of the revamped website include a comprehensive landing page offering intuitive navigation across tool categories, a ‘Your Jobs’ page providing a history of recently launched jobs with improved status tracking, redesigned tool webforms with detailed descriptions and enhanced user experience, and streamlined result pages with interactive features such as interactive summary tables, interactive visualisations including Nightingale MSA viewer and phylogenetic tree visualisations, and interactive graphical representations of Sequence Similarity Search tool outputs and functional predictions.
Overall, the new frontend of the Job Dispatcher website aims to provide users with a more efficient and enjoyable experience, facilitating easier navigation, improved job tracking, and enhanced visualization of results, ultimately enhancing the utility and accessibility of the bioinformatics tools and services provided by JD.
A summary of all the bioinformatics applications available through JD in 2024 is provided below:
| Category | Tools |
|---|---|
| Multiple Sequence Alignment | Clustal Omega, Kalign, MAFFT, MUSCLE, T-Coffee, MView, WebPrank |
| Pairwise Sequence Alignment | Needle, Stretcher, Water, Matcher, LALIGN, GeneWise, GGSEARCH2SEQ, SSEARCH2SEQ |
| Phylogeny Analysis | Simple Phylogeny |
| Protein Functional Analysis | InterProScan 5, PfamScan, Phobius, Pratt, RADAR, HMMER3 phmmer, HMMER3 hmmscan |
| RNA Analysis | Infernal cmscan, MapMi, R2DT |
| Sequence Similarity Search | NCBI BLAST+, PSI-BLAST, FASTA, SSEARCH, FASTM/S/F, GGSEARCH, GLSEARCH, PSI-Search, PSI-Search2 |
| Sequence Statistics | SAPS, Pepinfo, Pepstats, Pepwindow, Cpgplot, Newcpgreport, Isochore, Dotmatcher, Dottup, Dotpath, Polydot |
| Sequence Translation | Transeq, Sixpack, Backtranseq, Backtranambig |
| Sequence Format Conversion | Seqret, MView |
| Sequence Operation | Seqcksum |
| EMBOSS Suite | Needle, Stretcher, Water, Matcher, Transeq, Sixpack, Backtranseq, Backtranambig, Pepinfo, Pepstats, Pepwindow, Cpgplot, Newcpgreport, Isochore, Dotmatcher, Dottup, Dotpath, Polydot, Seqret |
| Dbfetch | Dbfetch (fetching data from 58 domains) |
Sequence datasets available through JD in 2024 are also provided below:
| Category | Data |
|---|---|
| UniProtKB protein sequences | UniProtKB, SwissProt, SwissProt Isoforms, TrEMBL, UniProtKB Taxonomic Subsets (13 subgroups, including: bacteria, archaea, eukaryota, SARS-CoV-2, etc.), Reference Proteomes, Representative Proteomes (15, 35, 55, 75), UniProt Reference (UniRef 50, 90 and 100), UniParc, Unimes, UniProtKB-PDB |
| Patent protein sequences | EPO, JPO, KIPO, UPSPTO |
| Structures of protein sequences | PDBe, AlphaFold DB |
| Protein families | Pfam, TIGRFAM, Superfamily, Gene3D, PIRSF, TreeFam, Pfam SARS-CoV-2 |
| Other protein sequences | Enzyme Portal, IntAct, IPD-IMGT/HLA, IPD-KIR, IPD-MHC, MEROPS (MP, MPEP and MPRO), ChEMBL, Quest for Orthologs |
| ENA nucleotide sequences | ENA sequences for Coding, Non-coding, Barcode, Geospatial, Ribosomal RNA and others (10 subgroups, including: Expressed Sequence Tag, Genome Survey Sequence, etc.) |
| Ensembl Genomes sequences | Genomes from Bacteria, Fungi, Plants, Metazoa, Protists, WormBase Parasite, SARS-CoV-2 |
| Structures of nucleotide sequences | PDBe |
| Other nucleotide sequences | IMGT/LIGM-DB, IMGT/HLA (CDS and genomic), IPD-KIR (CDS and genomic), IPD-NHKIR (CDS and genomic), IPD-MHC (CDS and genomic) |
| Additional entries available via Dbfetch | EMDB, PDBe-KB, MEDLINE, NCBI Taxonomy, EDAM ontology, HGNC |