BLAST

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Chapter 2: Biological Sequences

genetic element or selfish DNA (a phrase coined by Francis Crick). These entities are

a bit like the fleas and ticks of the genome: they copy and spread themselves within

and between genomes and are generally believed to do little for the host genome.

Selfish DNAs are usually further classified into three subcategories: transposons, ret-

roviruses, and retrotransposons. If you see these names in a BLAST report, you may

need to use a repeat filter.

Pseudogenes

One of the most confounding problems in similarity searches is the presence of

pseudogenes. As the name suggests, pseudogenes are “fake genes”; that is, they look

like they could encode a protein, but they aren’t functional. Pseudogenes come from

a variety of sources. A mutation that introduces a stop codon into a gene creates a

pseudogene, but more commonly, pseudogenes are created from some kind of dupli-

cation event. Sometimes, through various mechanisms, regions of a chromosome

may become duplicated. The extra copies of genes are generally free of selective pres-

sures and may become pseudogenes as they accumulate mutations. Duplication may

also result from repetitive elements that include neighboring DNA as they copy

themselves into new locations. In eukaryotes, a very common form of pseudogene ...