RNA Structure in Genomic Sequence:
Supplementary information for:
De novo prediction of structured RNAs from genomic sequences
Jan Gorodkin, Ivo L. Hofacker, Elfar Torarinsson, Zizhen Yao, Jakob H. Havgaard,
Walter L. Ruzzo
Methods
The main methods described in the paper were also applied in other studies and
here are some examples.
Exploiting sequence based multiple alignments for ncRNA screens
RNAz has also been used for genomic screens in for example:
Arabidopsis thaliana [
Song et al., 2009],
Nematodes [
Missal et al., 2006],
Drosophilids [
Rose et al., 2007],
Teleost fishes [
Rose et al., 2008],
Urochordates [
Missal et al., 2005],
yeast [
Steigele et al., 2007],
porcine EST sequences [
Seemann et al., 2007], as well as various bacteria.
EvoFold also was applied to screen
Drosophila
melanogaster
[
Stark et al., 2007].
Screen by pairwise local structural alignments
Foldalign has been used to search structural RNA motifs in prokaryotes,
amoeba, and humans [
Bidnenko et al., 2009,
Ahmed et al., 2006,
Vyas et al., 2009] and it has
further
been used to investigate structures of potential ncRNAs in bacteria and
for
phylogenetic analysis of beetles [
Sridhar et al., 2009,
Angelini and Jockusch, 2008].
Employing local multiple structural alignments
CMfinder was also recently applied to screen for ncRNAs in
prokaryotes [
Yao et al., 2007,
Weinberg et al., 2007]. Besides re-discovering
majority of the known
ncRNAs in prokaryotes [
Yao et al., 2007], the CMfinder-based pipeline
found 22
novel ncRNA motifs [
Weinberg et al., 2007], including
SAM-IV [
Weinberg et al., 2008],
S-adenosylhomocysteine [
Wang et al., 2008],
preQ1 [
Meyer et al., 2008],
molybdenum cofactor [
Regulski et al., 2008] and
cyclic di-GMP [
Sudarsan et al., 2008] riboswitches, subsequently validated
experimentally.
Resources:
Follow the links to the UCSC genome browser
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Angelini, D. and Jockusch, E. (2008).
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-
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-
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-
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(2007).
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-
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-
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A computational pipeline for high-throughput discovery of
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