Repeats

http://rsat.ulb.ac.be/help.retrieve-ensembl-seq.html
The presence of repetitive elements hampers the detection of motifs, especially for vertebrate genomes, because these repetitive sequences have a very distinct composition than the rest of the genome.

http://genes.mit.edu/Repeats.html
The presence of certain types of repetitive elements in a sequence may sometimes distort the results of GENSCAN. In particular, L1 elements are often predicted as genes. To avoid this potential problem, you may wish to pre-screen for repetitive elements with a program like RepeatMasker or censor which replace sequence segments matching any of a set of elements common to your organism (e.g., Alu, L1, etc.) by the same number of asterisks or `N's.

Another option is to filter out repeats after running GENSCAN, e.g. to screen GENSCAN predicted peptides against a database of repeat sequences translated in all six frames.

Rogozin et al. Brieifings in Bioinformatics. 2000
This model suggests that
most SINEs in the mammalian
genomes are pseudogenes, and not
capable of producing copies.


SINE can affect the
function and
recombination of
surrounding sequences


Thus, insertions of SINEs (as
well as other types of genome
mutations) can affect the long-term
adaptability of the species in various
ways.1,58



The database of repetitive elements
(Repbase)66


SINEs are almost always
a signture of non-coding
DNA



Incomplete SINEs or highly divergent
sequences can create some problems for
prediction.



Undiscovered repetitive elements, in
poorly characterised genomes, can
create serious problems for computational
functional mapping of sequences.


The presence of repetitive elements can
create serious problems for sequence
analysis, especially in homology
searches in nucleotide sequence
databases. It is difficult to interpret
database search results if the output is
saturated by a number of highly scored
matches with repetitive elements which
are widely present in nucleotide
sequence databases.