rDNA alignments

Luc Simon lsimon at alnus.for.ulaval.ca
Wed Jul 28 14:42:34 EST 1993

In article <01H0USXX3MZ60003UP at GW.AGR.CA>, EM609MBCPHL at NCCCOT7.AGR.CA

> Hi 
> Netters,
> I'm interested in amplifying ribosomal DNA including a least
> one spacer (for variability) in a wide range of eukaryotes
> (fungi, nematodes, insects). I'd like to design primers
> with varying specificities. does anyone have or know of
> any alignments of 18S, 5S and or 26S rDNA which would help
> in designing primers?
> Thanks,
> Pat Covello
> Central Plant Health Lab
> Agriculture Canada

One useful resource for this is the RDP (Ribosomal Database Project).
The Ribosomal Database Project (RDP) has been established to help
scientists and others utilize the large and rapidly growing collection
of ribosomal sequence data; at present the project is limited to
ribosomal RNA sequences.

The RDP offers or will offer:
    (1) alignments of the various classes of ribosomal RNA sequences,
    (2) software useful in manipulating the sequence data, and
    (3) various services to the user community.

The alignments are phylogenetically ordered (as far as possible), and
the user may select which sequences and which portions of the
sequences he/she wishes to have.  In addition some sequences are
offered in secondary structural representation.

The software includes several sequence editors/environments useful in
handling and analyzing the sequences, other programs for sequence and
phylogenetic tree display, and sequence analysis packages.

The services at present include phylogenetic analysis of sequences,
and probe checking, and will include probe design and sequence
alignment and assessment in the future.

The above are available via ftp (info.mcs.anl.gov) and/or electronic
mail:  rdp at mcs.anl.gov.

Its also accessible thru GOPHER, among other places at the Montreal's
MegaGopher and directly from University of Illinois:

There is now a dedicated RDP
ftp/gopher/email server  rdp.life.uiuc.edu (,
a/k/a rdpgopher.life.uiuc.edu).

Hope this helps!

Luc Simon
lsimon at alnus.for.ulaval.ca

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