TY - JOUR
T1 - The EMBL-EBI bioinformatics web and programmatic tools framework
AU - Li, Weizhong
AU - Cowley, Andrew
AU - Uludag, Mahmut
AU - Gur, Tamer
AU - McWilliam, Hamish
AU - Squizzato, Silvano
AU - Park, Young Mi
AU - Buso, Nicola
AU - Lopez, Rodrigo
N1 - Publisher Copyright:
© The Author(s) 2015.
PY - 2015
Y1 - 2015
N2 - Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi. ac.uk/Tools/sss/) such as BLAST, FASTA and PSISearch, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically throughWeb Services interfaces (https://www.ebi.ac. uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, Inter-ProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.
AB - Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi. ac.uk/Tools/sss/) such as BLAST, FASTA and PSISearch, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically throughWeb Services interfaces (https://www.ebi.ac. uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, Inter-ProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.
UR - http://www.scopus.com/inward/record.url?scp=84979851519&partnerID=8YFLogxK
U2 - 10.1093/nar/gkv279
DO - 10.1093/nar/gkv279
M3 - Article
C2 - 25845596
AN - SCOPUS:84979851519
SN - 0305-1048
VL - 43
SP - W580-W584
JO - NUCLEIC ACIDS RESEARCH
JF - NUCLEIC ACIDS RESEARCH
IS - W1
ER -