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. 2010 Jul;38(Web Server issue):W695-9.
doi: 10.1093/nar/gkq313. Epub 2010 May 3.

A new bioinformatics analysis tools framework at EMBL-EBI

Mickael Goujon  1 , Hamish McWilliam, Weizhong Li, Franck Valentin, Silvano Squizzato, Juri Paern, Rodrigo Lopez
Affiliations

A new bioinformatics analysis tools framework at EMBL-EBI

Mickael Goujon et al. Nucleic Acids Res. 2010 Jul.

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.

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Figures

Figure 1.
Figure 1.
Summary Table view of the results obtained when searching the sequence of mouse glomulin against the UniProtKB/Swiss-Prot database using SSEARCH.
Figure 2.
Figure 2.
Comparisons between the Visual output results obtained when searching the sequence of mouse glomulin against the UniProtKB/Swiss-Prot database using SSEARCH and NCBI BLAST, respectively.
Figure 3.
Figure 3.
Functional prediction view of the results obtained when comparing the sequence of putative bioactive lysophospholipid that was compared against UniProtKB/Swiss-Prot using NCBI BLAST.
See this image and copyright information in PMC

References

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