AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application.

ABSTRACT: Systematic Evolution of Ligands by EXponential Enrichment (SELEX) is a well established experimental procedure to identify aptamers - synthetic single-stranded (ribo)nucleic molecules that bind to a given molecular target. Recently, new sequencing technologies have revolutionized the SELEX protocol by allowing for deep sequencing of the selection pools after each cycle. The emergence of High Throughput SELEX (HT-SELEX) has opened the field to new computational opportunities and challenges that are yet to be addressed. To aid the analysis of the results of HT-SELEX and to advance the understanding of the selection process itself, we developed AptaCluster. This algorithm allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional

SUBMITTER: Hoinka J 

PROVIDER: S-EPMC4281958 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature