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© Oxford University Press

A new dynamic tool to perform assembly of Expressed Sequence Tags (ESTs)

Robert W. Gill 1,3, T.Charles Hodgman 1, Chris B. Littler 1, Marcus D. Oxer 1, Douglas S. Montgomery 2, Steve Taylor 1 and Philippe Sanseau 2,3

1Advanced Technology & Informatics Glaxo-Wellcome Medicines Research Centre Stevenage, Herts SGI 2NY, UK
2Genomics Research Units, Glaxo-Wellcome Medicines Research Centre Stevenage, Herts SGI 2NY, UK

3To whom correspondence should be addressed

MOTIVATION: Expressed Sequence Tags (ESTs) are short single-pass DNA sequences obtained from either ends of cDNA clones. To exploit these sequences efficiently, a dynamic. Web-tool has been developed which uses these data to perform fast virtual collating of cDNAs.

RESULTS: Starting with a query sequence, the user is able to identify related ESTs and extend the sequence of interest step by step, possibly to a full-length transcript. Graphical views of the clustering are used to monitor the progress of a particular ‘cloning’ project. Potential open reading frames are detected by positional base preference, and hyperlinks to other Worldwide Web sites allow the user to retrieve information relevant to each EST in a cluster (e.g. sequence traces, clone size, plate position). Apart from cDNA cloning, this tool also provides a mechanism for collating gene families and polymorphism sites.

AVAILABILITY: This tool is available at the following URL: http://www3.ebi.ac.uk/{small tilde}gill/ESTblast

CONTACT: E-mail: rwg23944{at}ggr.co.uk; psl4446{at}ggr.co.uk

Received on February 14, 1997; accepted on April 15, 1997

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