Development of Computational Tools for Searching Regulatory Sequences of the Transcription in Prokaryotic Cells

Carlos Andrés Pérez, Antonio Pérez, Juan Falgueras


This paper deals with a PERL pro­gram for tracking the DNA sequenc­es that join transcription factors regulating the genetic expression of prokaryotic cells. The gene sets where obtained from their expres­sions under the same environmental conditions. The model organism was the lactococcus lactis, an organism for which we possess its sequenced genome in gene bank format. The program found a larger number of possible regulatory sequences in the 5’ flanking region of the genes. The number of possible regulatory se­quences was also determined for the amount of genes that made up the set. The program also located flank­ing gene sequences which could also be involved in its regulation but at a translational level. The comparison of the results with patterns obtained experimentally, was done by means of nucleotide position weight matri­ces, getting around 50% regulating sequences which coincide with those reported in the databases, indicating good program prediction capability, if you account for the fact that most prokaryotic cell regulating sequences have yet to be characterized by ex­perimental methods.


Bioinformatics; PERL; transcription; translation; position weight matrix; transcription factors.



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