Anthology of Human Repetitive DNA
299
Currently, RU is released in the EMBL
and Fasta formats. Only the EMBL format
contains a detailed description and anno-
tation of every RU consensus sequence.
In addition, a version of RU manually tai-
lored for RepeatMasker is available. RU
contains several sections dedicated to sep-
arate eukaryotic species. Human TEs are
listed in the section ‘‘humrep.ref.’’ Most of
the abundant processed pseudogenes can
be obtained from the ‘‘pseudo.ref’’ library.
The ‘‘simple.ref’’ library contains the most
common simple repeat motifs.
Apart
from
Repbase
Update,
there
are other useful online resources for
studies of human repeats. Table 12 lists
selected databases
as
well
as
related
resources devoted to human repetitive
elements.
6.2
Programs for Detection and Analysis of
Repetitive DNA
There are two basic approaches for de-
tection of repetitive elements in bio-
logical sequences. The ±rst is based
on
the
detection
of
similarity
with
previously
known
repeats.
The
sec-
ond
de novo
approach is based on a
Tab. 12
Databases of human repeats, and related sources.
Database
URL description
Repbase Update
Update.html
De facto
the only specialized database of eukaryotic repetitive elements.
To date, Repbase Update contains consensus sequences and
annotation for more than 4000 different eukaryotic repetitive
elements. The content can be searched through sequence similarity
search on the Censor web server, or through the text search using
keywords.
HERVd
The Database of Human Endogenous Retroviruses (HERVs) maps all
known endogenous retroviruses in the human genome. Retroviruses
can be searched using several criteria such as family, length,
chromosome etc., or by fasta similarity search. Several characteristics
including the GC content, CpGs are calculated.
Human TE Insertion
The database lists known insertions of repetitive elements into the
human genome associated with human genetic diseases.
Exapted retrogenes
http://www-iF.uni-muenster.de/exapted-retrogenes/tables3.html
Examples of vertebrate regulatory elements, parts of coding regions or
genes generated by retroelements. Vertebrate genes generated by
retrosequences.
UCSC GoldenPath
The UCSC human genome assembly contains extensive annotation Fles
including tables with maps of repetitive elements in the human
genome.
Ensembl
The ensembl genome assembly contains extensive annotation Fles
including tables with maps of repetitive elements in the human
genome.
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