DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.

ABSTRACT:

Motivation

RNA structure is essential for the function of many non-coding RNAs. Using multiple homologous sequences, which share structure and function, secondary structure can be predicted with much higher accuracy than with a single sequence. It can be difficult, however, to establish a set of homologous sequences when their structure is not yet known. We developed a method to identify sequences in a set of putative homologs that are in fact non-homologs.

Results

Previously, we developed TurboFold to estimate conserved structure using multiple, unaligned RNA homologs. Here, we report that the positive predictive value of TurboFold is significantly reduced by the presence of contamination by non-homologous sequences, although the reduction is less than 1%. We developed a me

SUBMITTER: Zhu M 

PROVIDER: S-EPMC11507696 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature