Phi-Blast Search Using Multiple Patterns

Question

[hon.tran]

hi,

./ncbi-blast-2.2.27+/bin/psiblast -db testdb -query testquery -num_iterations 3 -phi_pattern patternFile

phi-blast takes only the last pattern from patternFile which looks as follows

ID pattern1 PA -P-x-G-x-[STA]-x-[NT]

ID pattern2 PA -H-x-[LS]-S

somebody knows why phi-blast does not take both patterns for search? thanks

Hon

Answer 1

[Pappu]

You can write a custom python script for this purpose.