A tool or webserver for building PSSM matrix I have some protein sequences and I want to build a position-specific scoring matrix (PSSM) for them and then upload this PSSM to NCBI PSI-BLAST. I used CHAPS program for this pupose but uploading the output PSSM gave me an error in NCBI PSI-BLAST. Do you know any tool or webserver for getting PSSMs for a group of protein sequences which then can work in NCBI PSI-BLAST?
This is a part of my PSSM file: 

PssmWithParameters ::= {
pssm {
    isProtein TRUE ,
    numRows 28 ,
    numColumns 131 ,
    byRow FALSE ,
    query
    seq {
        id {
            other {
                accession "WP_000208753" } } ,
        inst {
            repr raw ,
            mol aa ,
            length 131 ,
            seq-data
            ncbieaa "MTTKRKPYVRPMTSTWWKKLPFYRFYMLREGTAVPAVWFSIELIFGLFALKNGPEAW
AGFIDFLQNPVIVIINLITLAAALLHTKTWFELAPKAANIIVKDEKMGPEPIIKSLWAVTVVATIVILFVALYW" } } ,
    intermediateData {
        freqRatios {
            { 0, 10, 0 } ,
            { 564418841, 10, -10 } ,
            { 0, 10, 0 } ,
            { 11768571, 10, -9 } ,
            { 185838265, 10, -10 } ,
            { 31496547, 10, -9 } ,
            { 3872857, 10, -8 } ,
            { 291750464, 10, -10 } ,
            { 128450763, 10, -10 } ,
            { 759856221, 10, -10 } ,
            { 359173937, 10, -10 } ,
            { 179865517, 10, -9 } ,
            { 14537895, 10, -8 } ,
            { 212921456, 10, -10 } ,
            { 220554141, 10, -10 } ,
            { 368516324, 10, -10 } ,
            { 319343525, 10, -10 } ,
            { 426173953, 10, -10 } ,
            { 463659523, 10, -10 } ,
            { 817322186, 10, -10 } ,
            { 811693964, 10, -11 } ,
            { 0, 10, 0 } ,
            { 227810064, 10, -10 } ,
            { 0, 10, 0 } ,
            { 0, 10, 0 } ,
            { 0, 10, 0 } ,
            { 0, 10, 0 } ,
            { 0, 10, 0 } ,
            { 0, 10, 0 } ,
            { 768325726, 10, -10 } ,
            { 0, 10, 0 } ,
            { 1425562, 10, -8 } ,
            { 372685285, 10, -10 } ,
            { 466727421, 10, -10 } ,
            { 185741084, 10, -10 } ,
            { 427328646, 10, -10 } ,
            { 122594965, 10, -10 } ,
If you take a look at my answer in this BioStars post, you can generate a PSSM using AlignIO in Biopython: