UNLABELLED: When developing bioinformatical tools dealing with enzymatic activity, metabolism or enzymatic networks, the problem of the lack of a clear nomenclature for biochemical compounds often arises. This problem leads us to develop a small web-based tool (SNOW, Standard NOmenclature Wizard) which may help to find recommended and trivial names or the correct closest spelling for a query compound name, if it exists. AVAILABILITY: Web-based interface available at http://ibb.uab.es/snow/ SUPPLEMENTARY INFORMATION: http://ibb.uab.es/snow/snow_moreinfo.html

Abstract Motivation: The advent of genomics yields thousands of reading frames in search of function. Identification of conserved functional motifs in protein sequences can be helpful for function prediction. Results: A database and a classification of reported DNA-binding protein motifs has been designed. A program (‘TranScout’) has been developed for the detection and evaluation of conserved motifs in prokaryotic and eukaryotic sequences of proteins with a gene regulatory function. The efficiency of the program is shown in a benchmark against a database obtained from SWISS-PROT without the protein sequences used to train the program. All motifs were detected with a mean average sensitivity of 0.98 and a mean average specificity of 0.92. Availability: The program is freely available for use on the internet at http://luz.uab.es/transcout/. The user can find additional information at this site. Contact: [email protected]; [email protected] * To whom correspondence should be addressed. 2 Present address: Laboratorio de Biologı́a Estructural Computacional (GRIB), Universitat Pompeu Fabra, C/Doctor Aiguader, Barcelona 08003, Spain.