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Reducing the Space of Degenerate Patterns in Protein Remote Homology Detection
Found in: 2013 24th International Workshop on Database and Expert Systems Applications (DEXA)
By Matteo Comin,Davide Verzotto
Issue Date:August 2013
pp. 76-80
In biology the notion of degenerate pattern plays a central role for describing various phenomena. For example, protein active site patterns, like those contained in the PROSITE database, e.g. [FY]DPC[LIM][ASG]C[ASG], are in general represented by degenera...
 
Whole-Genome Phylogeny by Virtue of Unic Subwords
Found in: 2012 23rd International Workshop on Database and Expert Systems Applications (DEXA)
By Matteo Comin,Davide Verzotto
Issue Date:September 2012
pp. 190-194
With the progress of modern sequencing technologies a number of complete genomes is now available. Traditional motif discovery tools cannot handle this massive amount of data, therefore the comparison of complete genomes can be carried out only with ad hoc...
 
Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Matteo Comin,Davide Verzotto
Issue Date:July 2014
pp. 628-637
The cell-type diversity is to a large degree driven by transcription regulation, i.e., enhancers. It has been recently shown that in high-level eukaryotes enhancers rarely work alone, instead they collaborate by forming clusters of cis-regulatory modules (...
 
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