Plasmodium falciparum - Tandem Repeat Analysis Protocol

Experimental procedure

1. The file p_falciparum.fasta corresponds to the frozen data (November 23, 2004 http://plasmodb.org/restricted/data/P_falciparum/WG/nuc/) of Plasmodium falciparum genome.
   
   
2. Genome sequence FASTA file Genome complexity - 23,042,330 bp
   
   
3. The file was submitted to Tandem Repeats Finder (TRF) (Benson, 1999) program using the following parameters:
   2 5 7 80 10 25 1000.
   
   
4. TRF output files were analyzed by the Tandem Repeat Analysis Program (TRAP) using the following parameters:
   • Minimum period size of repeats - 1
   • Maximum period size of repeats - 6
   • Minimum identity percentage - 80
   • Create HTML - yes
   • Sorting - according to the total number of bases
     

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