COSMOS: Conserved Structural Motif
Search Tool Posttranscriptional regulation of gene expression is
gaining widespread attention as its significant contribution to dynamics of
gene regulation is being revealed. Cis-regulatory
elements that are involved in posttranscriptional regulation are mostly
structural motifs that reside within the untranslated region (UTR) of mRNA.
Identification of these motifs is, however, a challenging task. These
regulatory elements do not necessarily have conserved positions, meaning that
they are very elusive to alignment-based approaches. Furthermore, as both
structure and sequence are crucial elements of their identity, conventional
motif identification algorithms fail to find these structured motifs. COSMOS provides an alternative method
for identification of structural RNA motifs. The main assumption behind the
algorithm of COSMOS is that if a functional cis-regulatory element is present in the UTR of a gene, it can
most probably be found in the UTR of the orthologs of that gene as well,
regardless of its position. COSMOS thus searches for structural motifs whose
pattern of presence and absence in different genes is conserved across
species. The COSMOS package provides a code that has been optimized for rapid
analysis of millions of possible structural motifs in order to identify the
most conserved ones. It also contains accessory tools that allow downstream
analysis of the discovered motifs, such as identification and deletion of
overlapping (redundant) motifs. These tools can create data files that are
readable to other analysis tools such as GSEA. COSMOS
Developers: Hamed Shateri Najafabadi Reza Salavati Last updated on 2/16/2011 7:19:59 PM |