# 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 } ,

• Which error did it give you the NCBI PSI-BLAST? Could you paste here the image with the options used? What have you tried to overcome this problem?
– llrs
Jun 30 '17 at 14:15
• The error was: Message ID#9 Error: PSSM processing error: Incomplete PSSM with Parameters provided on input: missing score matrix
– Sara
Jun 30 '17 at 14:25
• So it seems that you need to provide the PSSM in certain format and CAPS didn't manage to create it in the expected format. Could you post the PSSM here (or in an accessible way) ? Now that I look in the help I couldn't find any reference to a specific format (just that it should be from their own output ...)
– llrs
Jun 30 '17 at 14:34
• I do not exactly know how to post PSSM file here. Could you please guide me how to load a file here?
– Sara
Jun 30 '17 at 14:51
• @Sara see formatting tools for help on formatting your posts. For things like this, you want to use code ({}) which uses a fixed-width font. Jun 30 '17 at 16:10

If you take a look at my answer in this BioStars post, you can generate a PSSM using AlignIO in Biopython: