This workshop furthered the goals www.selleckchem.com/products/Abiraterone.html of the consortium by making progress on several of the RNA structure mapping concepts elaborated upon during previous ROC meetings in Kona and in Strasbourg. In addition, it brought together members of the ROC with members of the Genomic Standards Consortium (GSC) [6], an open-membership organization working towards 1) implementing new genomic standards, 2) capturing and exchanging information expressed in these standards and 3) harmonizing information collection and analysis efforts across the wider genomics community. The aim of developing links with the GSC was to inform developers and curators of genomic and metagenomic software and resources of the standards for representing RNA secondary and 3D structures and alignments developed by ROC and to encourage collaboration to improve genomic annotations.
The overall structure of the meeting consisted of a working dinner, software presentations, a roundtable discussion on annotation challenges, and assembly of working groups to address these challenges. The major annotation issues that were identified included: 1) How can information that is useful for drawing/representing RNA structures be exchanged among different software programs and incorporated into different genomic and metagenomic web sites for display to end users? 2) How can information about covariance models automatically be used to infer correspondence groups? 3) How can information about structure mapping experiments be captured to facilitate automatic secondary structure inference and propagated and displayed in a way that is useful to end users? Software Presentations Eric Nawrocki provided an introduction to structural RNA homology search using Infernal (INFERence of RNA ALignment) [7].
He noted that searching DNA sequence for noncoding RNA (ncRNA) molecules is more difficult than searching for proteins, because ncRNA molecules are generally shorter than protein molecules and their alphabet is smaller, so conserved secondary structure of RNAs provides useful additional signal. Infernal scores Cilengitide the combination of consensus sequence and consensus structure using covariance models; this technique produces results that are more sensitive than either BLAST or basic hidden-Markov model-based approaches. A major drawback of the current implementation of Infernal is that it is computationally intensive, but acceleration remains a major goal of the project. Jesse Stombaugh presented a live demonstration of Boulder ALE (ALignment Editor) [8], a tool for manual examination and adjustment of multiple sequence alignments.