Our latest service update article titled The EMBL-EBI search and sequence analysis tools APIs in 2019 has been published in Nucleic Acids Research, Web Server Issue.
In this paper, we describe the various enhancements made recently to EBI Saerch and Job Dispatcher services. Additionally, examples of integration between the resources are provided, which aim to demonstrate the ‘Software as a Service’ (SaaS) capabilities of the APIs.
For those not so familiar with Job Dispatcher and EBI Search, the abstract should give a good idea what these are about:
The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.
New and updated bioinformatics tools available through Job Dispatcher in 2019. The OpenAPI user interface for these tools is available from: https://www.ebi.ac.uk/Tools/common/tools/help
| Category | Tools |
|---|---|
| Multiple Sequence Alignment | Clustal Omega, Kalign, MAFFT, MUSCLE, T-Coffee, MView and WebPRANK |
| Pairwise Sequence Alignment | Needle, Stretcher, Water, Matcher, LALIGN, and GeneWise |
| Phylogeny Analysis | Simple Phylogeny |
| [Protein Functional]Analysis (https://www.ebi.ac.uk/Tools/pfa/) | InterProScan 5, PfamScan, Phobius, Pratt, RADAR, HMMER3 phmmer and HMMER3 hmmscan |
| RNA Analysis | Infernal cmscan and MapMi |
| Sequence Format Conversion | Seqret and MView |
| Sequence Operation | Seqcksum |
| [Sequence Similarity]Search (https://www.ebi.ac.uk/Tools/sss/) | NCBI BLAST+, PSI-BLAST, FASTA, SSEARCH, FASTM/S/F, GGSEARCH, GLSEARCH, PSI-Search and PSI-Search2 |
| Sequence Statistics | SAPS, Pepinfo, Pepstats, Pepwindow, Cpgplot, Newcpgreport, Isochore, Dotmatcher, Dottup, Dotpath and Polydot |
| Sequence Translation | Transeq, Sixpack, Backtranseq and Backtranambig |
New and Updated Data resources available through Job Dispatcher in 2019.
| Category | Datasets |
|---|---|
| UniProtKB protein sequences | UniProtKB, SwissProt, SwissProt Isoforms, TrEMBL, UniProtKB Taxonomic Subsets (13 subgroups, including: bacteria, archaea, eukaryota, etc.), Reference Proteomes, Representative Proteomes (15, 35, 55, 75), UniProt Reference (UniRef 50, 90 and 100), UniParc, Unimes and UniProtKB-PDB |
| Patent protein sequences | EPO, JPO, KIPO, UPSPTO |
| Structures protein sequences | PDBe and PSI structure targets |
| Protein families | Pfam, TIGRFAM, Superfamily, Gene3D, PIRSF and TreeFam |
| Other protein sequences | Enzyme Portal, IntAct, IPD-IMGT/HLA, IPD-KIR, IPD-MHC, MEROPS (MP, MPEP and MPRO), ChEMBL and Quest for Orthologs |
| ENA nucleotide sequences | ENA sequence releases and updates for Coding, Non-coding, Barcode, Geospatial and others (10 subgroups, including: Expressed Sequence Tag, Genome Survey Sequence, etc.) |
| Ensembl Genomes sequences | Genomes from Bacteria, Fungi, Plants, Metazoa and Protists |
| Structures of nucleotide sequences | PDBe |
| Other nucleotide sequences | IMGT/LIGM-DB, IMGT/HLA (CDS and genomic), IPD-KIR (CDS and genomic) and IPD-MHC (CDS and genomic) |