This R script is made to convert the PFAM IDs from Blast result tables to interpretable descriptions and molecular function names of proteins
This tool works on blast result tables that were generated using the -outfmt 6 option, for example
blast_output_example.txt
...
D00420:119:HVWNHBCXX:2:1101:1137:2200 PF00145 35.088 57 36 1 20 190 61 116 1.7 32.7 D00420:119:HVWNHBCXX:2:1101:1137:2200 PF00145 35.088 57 36 1 201 31 61 116 1.7 32.7 D00420:119:HVWNHBCXX:2:1101:1473:2123 PF00888 25.532 47 29 1 2 142 516 556 0.81 33.9 D00420:119:HVWNHBCXX:2:1101:1473:2123 PF00888 25.532 47 29 1 189 49 516 556 0.81 33.9 D00420:119:HVWNHBCXX:2:1101:1922:2189 PF00124 97.059 34 1 0 172 273 1 34 6.74e-15 68.9 D00420:119:HVWNHBCXX:2:1101:1922:2189 PF00124 97.059 34 1 0 103 2 1 34 6.74e-15 68.9 D00420:119:HVWNHBCXX:2:1101:1805:2237 PF07528 62.500 48 18 0 261 404 1 48 1.98e-12 68.6 D00420:119:HVWNHBCXX:2:1101:1805:2237 PF07528 62.500 48 18 0 144 1 1 48 1.98e-12 68.6 D00420:119:HVWNHBCXX:2:1101:2391:2102 PF07729 29.688 64 37 2 32 199 30 93 0.51 34.3 D00420:119:HVWNHBCXX:2:1101:2391:2102 PF07729 29.688 64 37 2 207 40 30 93 0.51 34.3
...
The columns above correspond to:
-
qseqid query (e.g., gene) sequence id -
sseqid subject (e.g., reference genome) sequence id -
pident percentage of identical matches -
length alignment length -
mismatch number of mismatches -
gapopen number of gap openings -
qstart start of alignment in query -
qend end of alignment in query -
sstart start of alignment in subject -
send end of alignment in subject -
evalue expect value -
bitscore bit score
You can run the present tool by:
Rscript classify_blast_results_from_PFAM_database.R blast_output_example.txt 75 1e-5
where:
the first paremeter is the blast output file (blast_output_example.txt in this case)
the second parameter is the sequence identity cuttoff value (75% in this case)
the third parameter is the e-value cuttoff (1e-5 in this example)