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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 (  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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