I need to write a script that can do a blastp with an input xml file, then find and display the PDB codes of sequences that are homologous. The definition I'm using for homology is: 1. the HSP in the alignment with the highest e-value is less than .001; and 2. the total alignment length (not counting gaps) is 60% or more of the query length.
I'm still new to programming, and I'm quite stumped as to how to do this.
I'd really appreciate your help. Thanks!