300
Anthology of Human Repetitive DNA
search for characteristic properties of
particular repeats. Table 13 lists some
of the most popular programs devel-
oped
for
the
detection
of
repetitive
elements.
Similarity-based methods typically com-
pare a library of known repetitive se-
quences against genomic DNA using
general programs for sequence similar-
ity search such as blast, wublast or
cross
match. The repetitive library can
be any custom set of
repeats; how-
ever,
specialized
programs
nearly
ex-
clusively rely on consensus sequences
from Repbase.
De novo
detection methods
do not require prior knowledge of re-
peats
and
the
guiding
principle
of
this
approach
is
to
search
for
the
presence
of
multiple
copies
in
the
genome.
Standard
detection
programs
for
interspersed
repeats
use
similarity-
based
detection
of
repeats.
Censor
and MaskerAid require wublast, while
RepeatMasker uses the Smith-Waterman
algorithm implemented in cross
match.
For large quantities of data or for quick
searches, it is better to use Censor or
Tab. 13
Programs for detection of repetitive sequences in biological sequences.
Program (package)
URL description
Censor
Server.html
General package for similarity-based identiFcation of
interspersed and tandem repeats in both nucleic and amino
acid sequences. Requires wublast and Repbase Update repeat
libraries. Both online and local versions are
available.
RepeatMasker
General package for similarity-based identiFcation of
interspersed and tandem repeats in nucleic acid sequences.
Requires cross
match and Repbase Update repeat libraries.
Both online and local versions are available.
MakerAid
Program performs a similarity-based detection of interspersed
and tandem repeats in nucleic acid sequences. Can be used
with RepeatMasker for fast repeat identiFcation. Requires
wublast and external repeat libraries. Local versions only.
Tandem repeat Fnder
An excellent program to for
de novo
detection of tandem repeats
in DNA sequences. Both online and local versions available.
Satellites
Program to for
de novo
detection of tandem repeats in DNA
sequences. Online version only.
Sputnik
http://espressosoftware.com:8080/esd/pages/sputnik.jsp
Scans for 2–5 long tandem repeats using
de novo
search.
EMBOSS
A general open source package for analysis of biological
sequences. Two included programs etandem and
equicktandem detect tandem repeats using
de novo
search.
Local versions only.
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