Conversion of NCBI BLAST+ tblastn results to PSL format

Wilson Leung

Last Update: 04/24/2016

Version information

Data sources

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.

Conversion protocol

  1. Create BLAST database for the assembly

    makeblastdb -in Dbia3.fa -dbtype nucl
  2. 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
  3. Convert results into PSL format

    blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl
  4. Convert PSL output into BED format

    pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed

Output files