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.
Hamed Shateri Najafabadi
Last updated on 2/16/2011 7:19:59 PM