UNLABELLED: The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks. WGE is open, extensible and can be set up to compute and present CRISPR sites for any genome. AVAILABILITY AND IMPLEMENTATION: The WGE database is freely available at www.sanger.ac.uk/htgt/wge CONTACT: : [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

D. Akrigg, T.K. Attwood, A.J. Bleasby, J.B.C. Findlay, A.C.T. North, N.A. Maughan, D.J. Parry-Smith, D.N. Perkins, J.C. Wootton; SERPENT—an information sto

A new protein sequence analysis package, ADSP, is described, of which the SOMAP Screen-Oriented Multiple Alignment Procedure forms an integral part. ADSP (Algorithms and Data Structures for Protein sequence analysis) incorporates facilities to generate potent pattern-recognition discriminators and offers four algorithms with which to scan any NBRF format sequence database: the package has been designed, in particular, to interface with the OWL composite sequence database, one of the largest, distributed non-redundant sources of sequence data of its kind. The system incorporates a powerful method for compound feature analysis, which provides the basis for characterizing and predicting the occurrence of complete protein superfamilies and for pinpointing the emergence of related sub-families. Used iteratively, the approach allows diagnostic performance to be rigorously refined and its efficacy to be assessed both qualitatively and quantitatively, and results in the generation of refined structural or functional features suitable for entry into a database: this compilation of characteristic signatures is distinct from, but complementary to, widely used compendia of pattern templates such as PROSITE.

A novel interactive method for generating multiple protein sequence alignments is described. The program has no internal limit to the number or length of sequences it can handle and is designed for use with DEC VAX processors running the VMS operating system. The approach used is essentially one of manual sequence manipulation, aided by built-in symbolic displays of identities and similarities, and strict and 'fuzzy' (ambiguous) pattern-matching facilities. Additional flexibility is provided by means of an interface to a publicly available automatic alignment system and to a comprehensive sequence analysis package.