title: A new bioinformatics analysis tools framework at EMBL-EBI.
abstract: The EMBL-EBI provides access to various mainstream sequence analysis applications. These include sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignment tools such as ClustalW, T-Coffee and MUSCLE. Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes. We present here a new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface. These services are available over the web and via Web Services interfaces for users who require systematic access or want to interface with customized pipe-lines and workflows using common programming languages. The framework features novel result visualizations and integration of domain and functional predictions for protein database searches. It is available at http://www.ebi.ac.uk/Tools/sss for sequence similarity searches and at http://www.ebi.ac.uk/Tools/msa for multiple sequence alignments.
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Mickael
authors.initials: M
authors.lastname: Goujon
authors.forename: Hamish
authors.initials: H
authors.lastname: McWilliam
authors.forename: Weizhong
authors.initials: W
authors.lastname: Li
authors.forename: Franck
authors.initials: F
authors.lastname: Valentin
authors.forename: Silvano
authors.initials: S
authors.lastname: Squizzato
authors.forename: Juri
authors.initials: J
authors.lastname: Paern
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Lopez
mesh_terms: D019295:Computational Biology; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020407:Internet; D016415:Sequence Alignment; D017421:Sequence Analysis; D012984:Software