Methods
BLAST alignments are performed using BioPerl’s StandAloneBlast
package. This package uses a preinstalled local copy of BLAST to
generate BLAST alignment reports. The Database of Annotated P.
falciparum genes comes from PlasmoDB (http://www.plasmodb.org).
Users are asked to specifiy the query file, database to search against,
and the e-value cutoff. The cut-off used to generate the included
materials is 1x10-10. The low-complexity filter was left on,
removing noise caused by low complexity sequences (see e.g. figure 5).
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