To compare test sequences and pssm

1) Format test sequences file, do this just once

./makeblastdb -in d2jaka1.fasta -out d2jaka1.db -dbtype prot

2) execute psi-blast for each PSSM in the train list.

Example: ./psiblast -db d2jaka1.db -in_pssm psiblastModels/d2nppb1.pssm -out test.txt -outfmt 6

The parameter -outfmt 6 save the output file in a tabular format, this is what you find in each column. 1st column = Query_Identifier 2sd column = PSSM_Identifier 3rd column = sequence Identity 4th column = Query Length 5th column = it is not important for us 6th column = it is not important for us 7th column = start position in the query 8th column = end position in the query 9th column = start position in the PSSM 10th column = end position in the PSSM 11th column = evalue 12th column = Bit score (we will use this as sequence score, we look for the highest bit score)

julibinho / fastClade

Install PSI-BLAST #1

1) Format test sequences file, do this just once

2) execute psi-blast for each PSSM in the train list.