NOTE: The following information is obsolete, since NCBI BLAST server was
updated to have one additional format option for PSSM - PssmWithParameters.
This displays the PSSM in ASN.1 scoremat format, which can be uploaded for
PSI-BLAST search, or for use locally in standalone blastpgp.
The following steps can be used to convert the web PSI-BLAST generated PSSM file locally:
a. Save the content to a text file
b. Remove the PSSM:digits line
c. Remove the newline characters
d. Convert the string to binary and output to a file
In perl, we can use the following code block to achieve this:
while (/(..)/){
$string=chr(hex($1));
print $string; }
e. Decompress the resulting binary file using the bzip2 utility
f. Convert the resulting file with asntool using the following commandline:
asntool -m PSSM.asn -M blstspc.asn,asn.all -d converted_file -p out.txt
Note: asntool is available by compiling the NCBI C toolkit. Its C++ equivalent datatool is available in precompiled form from NCBI ftp site. However, PSSM.asn and blstspc.asn are not available to the public at this time.