FindPTM

FindPTM has been developed to localize phosphates or any other post traductionnal modifications (PTM) positions in proteins sequences starting from the PTMs positions in peptides sequences and the proteins accession numbers.

FindPTM align peptides sequences on their corresponding proteins sequences and calculates the PTMs positions on the proteins sequences. FindPTM can process an unlimited number of peptides in an unlimited number of files at a rate of more than 3000 peptides/sec on a Core i7 processor.

FinPTM is compatible with Uniprot fasta files. FindPTM output is directly compatible with KEA2 software for phosphosites analysis. Detailed PTMs localisation files are produced as well.

Manual :

The software was written in GO and compiled for Linux and Windows 64 bits. The software can be compiled for other platforms on request.

1- unzip the software

The folder structure is :

FindPTM/

├── data

├── fasta

├── KEA2

├── results

└── sequence

2- copy your Fasta database in the “fasta” directory. FindPTM is compatible with Uniprot format. The name of the sequence must start by >sp|ACC| or >tr|ACC| where ACC is the accession number of the protein

3- copy your peptides table in the “data” directory, one item per line and TAB separator.

- first row of the table : column names : ACC Peptide Position

- first column : accession numbers

- second column : peptides sequences in uppercase

- third column : PTM positions in the peptide sequence

For example :

FindPTM supports one PTM/row. If a peptide contains more than one PTM, the row must be duplicated :

Acc SEQUENCE PTMpos1

Acc SEQUENCE PTMpos2

...

4- Linux : execute the software by the command : ./Linux_find_ptm_pos-014.bin in the FindPTM directory

Windows : double click on win_find_ptm_pos-014.exe

5- PTMs positions in KEA2 format are in the KEA2 folder

A detailed results table is in the result folder

The positions of the PTMs on proteins sequences are in the sequence directory with "-" for each peptide amino acid and "|" for the PTMs.