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Bioinformatics Vol. 18 no. 10 2002
Pages 1396-1397
© 2002 Oxford University Press

Applications Note

GENOTRACE: cDNA-based local GENOme assembly from TRACE archives

Eugene Berezikov 1, Ronald H.A. Plasterk 1 and Edwin Cuppen 1,*

1 Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands

Received on March 14, 2002 ; revised on May 2, 2002 ; accepted on May 5, 2002

Summary: GENOTRACE identifies the genomic organization for a cDNA using raw data from genome sequencing projects in progress (trace archives). Local genomic contigs are generated, allowing for example the design of PCR primers in intronic sequences to amplify coding regions of a gene, needed for example for mutation or SNP detection.

Availability: The package and examples of output files can be downloaded from http://rat.niob.knaw.nl/GENOTRACE

Contact: ecuppen{at}niob.knaw.nl

* To whom correspondence should be addressed.


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