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Bioinformatics Vol. 18 no. 4 2002
Pages 597-607
© 2002 Oxford University Press

TranScout: prediction of gene expression regulatory proteins from their sequences

Daniel Aguilar 1, Baldomero Oliva 1,2, Francesc X. Aviles 1 and Enrique Querol 1,*

1 Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain

Received on July 20, 2001 ; revised on October 10, 2001 ; accepted on November 6, 2001

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: Enric.Querol{at}uab.es; boliva{at}imim.es

* To whom correspondence should be addressed.

2 Present address: Laboratorio de Biología Estructural Computacional (GRIB), Universitat Pompeu Fabra, C/Doctor Aiguader, Barcelona 08003, Spain.


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