jeisen at KIMURA.STANFORD.EDU (Jonathan Andrew Eisen) writes:
>Jim Garey asks about sequence alignments of rRNA
>A few citations for using secondary structure information for the alignment
>of rRNA primary sequences are
> R. Gutell et al. Prog. Nucl. Acids Res. Mol. Biol. 32:155-216
> Woese, C et al. 1983. Microbiol. Rev. 47:621-669.
> Neefs et al. 1990. Nucl. Acids. Res. 18:2237-2317.
>Essentially the way it is done (or at least the way I've done it) is to align
>highly conserved regions of primary structure first. Then new sequences can
>be overlayed onto the modeled secondary structure of a known sequence (such as
>E. coli). Nucleotides at identical regions of the secondary structure can then
>be aligned in the primary structure. Of course you can run into lots of
>problems such as differences in secondary structure. For a simple example - if
>you have three sequences -
> 1 2 3
> A A A G A A
> G G A G A G
> A G A G A G
> G-C G-C G-C
> T-A A-T A-T
> A-T A-T A-T
>The position of the gap (due to the extra nucleotide in 3) may be somewhat
>hard to determine.
>1 ATGAGA-AGGCAT 1 ATGAGA-AGGCAT
>2 AAGAAA-GGGCTT or 2 AAGAAAG-GGCTT
>3 AAGAAAGAGGCTT 3 AAGAAAGAGGCTT
>It gets worse with more sequences> Usually, regions like these are left out of
>phylogenetic reconstructions because of the difficulty in the alignment. But
>they do not constitute the majority of sites.
>Jonathan A. Eisen
>Department of Biological Sciences
>Stanford, CA 94305-5020
>jeisen at kimura.stanford.edu
Jonathan (and others),
There is a (rather crude) mechanism available in GDE that allows you to
test for a proposed secondary structure within a given alignment. The
function is labeled Highlight Helix under the DNA/RNA menu. Try out
the demo data file HelixExampletRNAs to see how to set it up. It will
show all base pares that differ from the proposed 2ndary structure. It
will not hwever automatically align based on 2ndary structures.
P.S. GDE is available from megasun.bch.umontreal.ca through gopher