Rfam

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). Conserved RNA structures (*.dot) of human have been parsed from multiple-alignment files (*.seed)

Rfam database is located in /150T/zhangqf/GenomeAnnotation/Rfam

seed

The seed alignments are hand curated and aligned using available sequence and structure data, and covariance models are built from these alignments using the INFERNAL v1.1.2 software suite (http://infernal.janelia.org). It is a .stockholm file

You can parse conserved structures for all kinds of species with this file

seed file is located in /150T/zhangqf/GenomeAnnotation/Rfam/14.1/Rfam.seed

human conserved structures

Conserved structures from human have been parsed with python script in Parsed_Structure

dot file is located in /150T/zhangqf/GenomeAnnotation/Rfam/Parsed_Structure/human.dot