July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 9: BLAST Protocols
searches with a “compressed” sequence. This enables it to find nested repeats. If
your favorite genome is supported by RepeatMasker, it is probably better to use this
software than write your own. However, if you want/need to do your own repeat
masking, you will find that Bioperl tools are an enormous help.
Contaminant Detection
This protocol departs from the usual format because it is especially difficult and
requires more than a single BLAST search. Contaminants come in many forms.
Some, such as mitochondrial DNA mixed with nuclear DNA, are easily detected
with near-identity parameters. But cross-species contamination is very difficult to
detect. If you find an exact match between two genomes, is it contamination or a
highly conserved region? There’s no simple answer. Some genomes, however have
specific signatures. For example, the human genome has many primate-specific Alu
repetitive elements. If you find many Alu elements in a database of corn sequence,
it’s probably a contaminant.
The most critical part of contaminant detection is having representative databases.
You can’t find contaminants for which you have no sequences. On the other hand, if
your sequence database is too large, you may spend an inordinate amount of time
looking for contaminants.
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