blast_script_careyBMCG.rtf

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\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural\partightenfactor0

\f0\fs22 \cf0 \CocoaLigature0 \
makeblastdb -in PlasmoDB-28_Pfalciparum3D7_AnnotatedTranscripts.fasta -parse_seqids -dbtype nucl -input_type fasta\
\
blastn -db PlasmoDB-28_Pfalciparum3D7_AnnotatedTranscripts.fasta -query seqs_rev_complement.fa -out blast_output_pf_e0001 -evalue .0001 -task blastn -reward 1 -dust yes -penalty -3 -gapopen 5 -gapextend 2 -outfmt 10\
\
blastn -db PlasmoDB-28_Pfalciparum3D7_AnnotatedTranscripts.fasta -query seqs_rev_complement.fa -out blast_output_pf_e0001_standard -evalue .0001 -task blastn -reward 1 -dust yes -penalty -3 -gapopen 5 -gapextend 2}