Anthology of Human Repetitive DNA
301
MaskerAid, since they are much faster
than cross
match-based RepeatMasker.
RepeatMasker
and
MaskerAid
are
restricted
to
nucleic
acid
sequences
only. Censor, on the other hand, can
perform virtually any similarity search
implemented in the wublast package,
including translated searches, and can
even detect repetitive elements in protein
sequences. All these programs produce
maps of repetitive elements in query
sequences, with the exact position of
each repeat. These three programs also
‘‘mask’’ sequences, that is, they replace
detected repeats by special characters,
usually by ‘‘N’’ for nucleic and ‘‘X’’
for protein sequences. Such masking
is essential for many database searches
or gene predictions. Moreover, all these
programs detect the most frequent simple
repeats.
U
n
l
i
k
ei
nt
h
ec
a
s
eo
fi
n
t
e
r
s
p
e
r
s
e
d
repeats,
de novo
detection is the pri-
mary approach in the analysis of sim-
ple
repeats.
There
are
several
pack-
ages for the detection of microsatellites
with short unit sizes, but for minisatel-
lites with large units there are only a
few suitable programs. In such situa-
tions, Tandem Repeat Finder can be
applied.
In summary, for routine detection of
known repeats it is best to use Cen-
sor, RepeatMasker, or MaskerAid with
appropriate repeat libraries (Repbase Up-
date libraries). These programs also detect
the majority of simple sequence repeats,
particularly the most abundant microsatel-
lites. Specialized analysis of simple se-
quence repeats may involve specialized
de novo
detection programs. The major-
ity of programs listed in Table 13 can be
installed only on Linux/Unix-related sys-
tems. Users of other operating systems
may use several programs that have on-
line submission forms, as speci±ed in
Table 13.
See also
Genetics, Molecular Basis
of;
Genomic
Sequencing
(Core
Article).
Bibliography
Books and Reviews
Batzer, M.A., Deininger, P.L. (2002) Alu repeats
and human genomic diversity,
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Berg, D.E., Howe, M.M. (Eds.) (1989)
Mobile
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Cof±n, J.M., Hughes, S.H., Varmus, H.E. (Eds.)
(1997)
Retroviruses
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o
l
dS
p
r
i
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gH
a
r
b
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Cooper, D.N. (2003)
Encyclopedia of The Human
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Wilkinson, D.,
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