Wilson Leung
Last Update: 04/24/2016
For testing purposes, the database consists of only contig1 in the Dbia3 assembly while the protein sequences correspond to the three isoforms of the D. melanogaster ci gene in contig1. The protein sequences are available through FlyBase.
Create BLAST database for the assembly
makeblastdb -in Dbia3.fa -dbtype nucl
Perform tblastn search and output results in XML format
tblastn -outfmt 5 -db Dbia3.fa -query ci.pep -out tblastn_Dbia3_ci.xml -evalue 1e-2
Convert results into PSL format
blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl
Convert PSL output into BED format
pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed