Rna Screen Resources

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See also:

Resources for non-coding RNA computational screens

I'm going to call them ncRNAs for now, but the nomenclature debate (non-coding vs structural vs functional RNA) rages on.

Reviews

How to identify ncRNAs

Any evidence on what properties of ncRNAs can be used to build a ncRNA classifier.

Conserved secondary structure

What can I even cite for this? It seems that "mutations that conserve RNA secondary structure is evidence of a ncRNA" is taken as a given by everyone.

Free energy change of folding

Do ncRNAs have a lower free energy of folding than non-ncRNAs of similar nucleotide and/or dinucleotide composition? Can that be used to build a classifier?

Development of computational methods

A lot of these papers have a genome screen component. However, if the primary focus of the paper is method/tool development, it goes here instead of the "genome screen" section.

General

A lot of methods/tools from the Rna Structure Prediction Resources page can be used to detect conserved secondary structures, and therefore (in theory) serve as ncRNA detectors. The papers below are only for those methods that have been applied and more-or-less benchmarked as ncRNA finders.

Also, a lot of these are based on prior work described in Rna Structure Prediction Resources.

  • EvoFold
    •  ??? (TODO: is there a separate paper for this, or just the genome screen one? is it an extention of RNAdecode?)

Family-specific

CAVEAT: this section may be severly incomplete!

Database search

Any database search tool should, in theory, be usable as a screening tool - just make the database or query out of your genome and search using known families! So, the database search stuff is described here: Rna Structure Prediction Resources#Database_search

Genome screens

A lot of these papers also discuss how the computational tools/methods for ncRNA discovery were developed. However, if the primary focus of the paper is ncRNA discovery, it goes here instead of the "computational methods for identifying ncRNAs" section.

For all types of ncRNAs

TODO: why do I feel like I'm leaving something out... must consult Benasque notes...

For specific ncRNA families

CAVEAT: this section may be severly incomplete!

For microRNAs

There are probably more of these than three gods can count...

For snoRNAs

Functional annotation

See also: Rna Structure Prediction Resources#Clustering

Datasets of knowns

We need these to see if computational methods are finding anything biologically meaningful.

Known ncRNAs

Genome annotations

Sequence databases

Experimentally-detected transcripts

TODO: all the transcriptome papers should go here.

TODO: Need to categorize

Orphans (interesting, but how to categorize?)

Stuff I haven't even barely read yet, but it looks interesting

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-- Created by: Andrew Uzilov on 12 May 2007