toms@fcs260c2.ncifcrf.gov (Tom Schneider) (12/08/90)
Archive-name: bionet/molbio/delila/1990-12-06
Archive-directory: ncifcrf.gov:/pub/delila/ [129.43.1.11]
Original-posting-by: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Original-subject: Sequence Logos and Delila Archive
Reposted-by: emv@ox.com (Edward Vielmetti)
A set of programs for analysis of aligned sequences is now available by
anonymous ftp (file transfer protocol) at ncifcrf.gov in the directory
'pub/delila'. Further information is in a 'README' file, and the available
files are listed in 'README.logo.Z', 'README.delila.Z' and 'README.misc.Z'.
All files are comressed, except 'README'.
The files are also available to people on BITNET from Dan Davison
(davison@uh.edu) on "gene-server%bchs.uh.edu@CUNYVM" (many thanks to Dan for
this service).
The programs are part of the Delila System [1,2], and contain the Sequence Logo
programs recently described in [2].
The abstract for [3], describing Sequence Logos is:
A graphical method is presented for displaying the patterns in a set of aligned
sequences. The characters representing the sequence are stacked on top of each
other for each position in the aligned sequences. The height of each letter is
made proportional to its frequency, and the letters are sorted so the most
common one is on top. The height of the entire stack is then adjusted to
signify the information content of the sequences at that position. From these
`sequence logos', one can determine not only the consensus sequence but also
the relative frequency of bases and the information content (measured in bits)
at every position in a site or sequence. The logo displays both significant
residues and subtle sequence patterns.
Have fun! If you have any problems, please contact me.
Tom Schneider
National Cancer Institute
Laboratory of Mathematical Biology
Frederick, Maryland 21702-1201
toms@ncifcrf.gov
References:
[1]
@article{Schneider1982,
author = "T. D. Schneider
and G. D. Stormo
and J. S. Haemer
and L. Gold",
title = "A design for computer nucleic-acid sequence storage, retrieval and
manipulation",
journal = "Nucl. Acids Res.",
volume = "10",
pages = "3013-3024",
year = "1982"}
[2]
@article{Schneider1984,
author = "T. D. Schneider
and G. D. Stormo
and M. A. Yarus
and L. Gold",
title = "Delila system tools",
year = "1984",
journal = "Nucl. Acids Res.",
volume = "12",
pages = "129-140"}
[3]
@article{Schneider.Stephens.Logo,
author = "T. D. Schneider
and R. M. Stephens",
title = "Sequence Logos: A New Way to Display Consensus Sequences",
journal = "Nucl. Acids Res.",
volume = "18",
pages = "6097-6100",
year = "1990"}