Is it possible to use a fasta with protein sequences to predict signal peptide and TM without using signap, TMHMM, phobius ? How can i reproduce- calculate information about signal peptide presence or number of transmembrane helices ? I would like to get similar results like the features Phobius_TM ,Phobius_SP, SignalP_D, TMHMM_TM but without using those programs. Do you think it is possible ?
It is most definitely possible. I suggest you read the papers describing the programs and you will get an idea about the datasets they used, and how predictive models were developed. It is up to you whether you want to use the same data and modeling techniques, as pretty much any modern machine learning tool can be used for this task.