TranScout: prediction of gene expression regulatory proteins from their sequences.
BACKGROUND
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.


BACKGROUND
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.
Aguilar
Daniel
D
Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
Oliva
Baldomero
B
Aviles
Francesc X
FX
Querol
Enrique
E
D000465:Algorithms; D020816:Amino Acid Motifs / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000145:classification* / Q000235:genetics*; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D005786:Gene Expression Regulation / Q000235:genetics*; D016680:Genome, Bacterial; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods
D004268:DNA-Binding Proteins