NCBI/GenBank BLAST Output XML Parser Tool

We describe a small freely available computer script to extract ‘real world’ sequence descriptions from the BLASTX results from sequences generated by the stand-alone ncbi­blast­2.2.26 suite of tools (available from NCBI/GenBank). Our Python (2.7) script is intended to make name extraction feasible for thousands, of hundreds of thousands, of sequences such as that generated by BLASTX analysis of RNA-Seq (transcriptome) obtained cDNAs from next generation sequencing (NGS) experiments. This script facilitates the interrogation of the large BLASTX output of a transcriptome experiment by familiar tools such as Microsoft Excel, or LibreOffice Calc. The script was written and tested on the Linux operating system (Ubuntu 12.04 LTS), but should work in any Python 2.7 compatible environment. We include some example files and help documentation.