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Dst - Locate human repeats
Tandem Repeats Finder
Large Dot Plots
REPuter - Fast Computation of Maximal Repeats in Complete Genomes
RepeatMasker - mask out repeat sequences
CENSOR - mask out repeat sequences
Dst - Locate human repeats
Two search modes are available: a search for human repeats using the
file BR3X and a self-homology search that will find repeats more than
2kb apart. The images produced here after searching the repeat database
are simplified versions of those produced by the stand alone program.
Tandem Repeats Finder
A tandem repeat in DNA is two or more adjacent, approximate copies of a
pattern of nucleotides. Tandem Repeats Finder is a program to locate
and display tandem repeats in DNA sequences. In order to use the
program, the user submits a sequence in FASTA format. There is no need
to specify the pattern, the size of the pattern or any other parameter.
The program's analysis is sent back to the user's web browser as two
files, a summary table file and an alignment file. The summary table
contains information about each repeat, including its location, size,
number of copies and nucleotide content. Clicking on the location
indices for one of the table entries opens a second web browser that
shows an alignment of the copies against a consensus pattern. The
program is very fast, analyzing sequences on the order of .5Mb in just a
few seconds. Submitted sequences may be up to 5Mb in length. Repeats
with pattern size in the range from 1 to 500 bases are detected.
Large Dot Plots
This page accesses a very fast dot plot algorithm designed for large DNA
sequences. This demonstration only allows a sequence to be compared
with itself. The algorithm uses a word size of eight and remaps the the
matches onto a 500x500 grid. As the query becomes very large it is
necessary to set a threshhold for plotting (the cutoff score below). If
the cutoff is not raised, an interesting effect is observed where the
plot is largely black and the only light areas are regions of unusual
sequence organization like the ones found by Zinfo.
The default output is curently a postscript file that will be displayed externally to the WWW browser. The gif conversion is not currently producing a high quality image. This program is derived from an X-windows based interactive version that saves the internal mapping so that changes in the cutoff score can be displayed rapidly.
REPuter - Fast Computation of Maximal Repeats in Complete Genomes
REPuter computes all maximal duplications and reverse, complemented and
reverse complemented repeats in a DNA input sequence.
RepeatMasker - mask out repeat sequences
RepeatMasker screens DNA sequences in fasta format against a library of
repetitive elements and returns a masked query sequence ready for
database searches as well as a table annotating the masked regions.
CENSOR - mask out repeat sequences
The CENSOR web server allows users to have query sequences aligned against a re$
collection of human or rodent repeats (Jurka, et al., 1992; Jurka, 1995b). The $
are then"censored". Censoring means replacing the aligned portions with x's in$
sequences. The server automatically classifies all known repeats and adds the c$
report.
The query sequence(s) must be in Stanford/IG format. A Stanford/IG sequence beg$ more, sequence description or comment lines which begin with a semi-colon,";".$ comments is a single line with the sequence's locus name (up to 12 characters).$ one or more lines of sequence data, these may be lower- or upper-case.
Any Comments, Questions? Support@hgmp.mrc.ac.uk