I am third year Biotechnology student and I need to predict beta-barrell transmembrane proteins in whole proteome (3600~ proteins) for my engineering thesis. I found one program, but I need to use multiple MSA generated by PSI-BLAST with one multifasta file. I have MSA from PSI-BLAST, but it is 3600~seperate files for each protein. Is there anyway to run it one after another? For example to run that program I need to type in terminal: "./predictionprogram.sh protein1sequence.fasta profileofprotein1.prof" and it would be great if I could just type it once and program would load each profile file one after another but use one multlifasta sequence of whole proteome.
Thanks for help!
(PS: sorry for my English, it isn't my first language, I hope I was clear with my question)