# Data Provenance for PMScanR Example Files

This document describes the origin and generation of data files
located in the `inst/extdata/` directory of the PMScanR package.

## File: hemoglobins.fasta

* **Source:** Example sequences,  for hemoglobin proteins.
    * ("Manually created representative sequences for demonstration.")*
* **Generation/Processing Date:** *("2023-03-18")*
* **Processing Steps:** *("Sequences were formatted into a multi-FASTA file.")*
* **Original Licensing:** *("GPL-3")*

## File: out_Hb_psa.txt

* **Source:** This file is example output from running the PROSITE ps_scan tool (PSA format).
    * It was generated by running `ps_scan.pl` (version 2025_02, obtained from [https://ftp.expasy.org/databases/prosite/ps_scan/](https://ftp.expasy.org/databases/prosite/ps_scan/)) on the `hemoglobins.fasta` file using `prosite.dat` (version 2025_02, obtained from [https://ftp.expasy.org/databases/prosite/](https://ftp.expasy.org/databases/prosite/)).
* **Generation/Processing Date:** *("2023-03-18")*
* **Processing Steps:** Raw output from ps_scan.
* **Original Licensing:** PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License.

## File: out_Hb_gff.txt

* **Source:** This file is example output from running the PROSITE ps_scan tool (GFF like format).
    * It was generated by running `ps_scan.pl` (version 2025_02, obtained from [https://ftp.expasy.org/databases/prosite/ps_scan/](https://ftp.expasy.org/databases/prosite/ps_scan/)) on the `hemoglobins.fasta` file using `prosite.dat` (version 2025_02, obtained from [https://ftp.expasy.org/databases/prosite/](https://ftp.expasy.org/databases/prosite/)).
* **Generation/Processing Date:** *("2023-03-18")*
* **Processing Steps:** Raw output from ps_scan.
* **Original Licensing:** PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License.

## File: PROSITEoutput.txt

* **Source:** This file is example output from running the PROSITE ps_scan tool.
*   * It was generated by running `ps_scan.pl` (version 2025_02, obtained from [https://ftp.expasy.org/databases/prosite/ps_scan/](https://ftp.expasy.org/databases/prosite/ps_scan/)) on the `hemoglobins.fasta` file using `prosite.dat` (version 2025_02, obtained from [https://ftp.expasy.org/databases/prosite/](https://ftp.expasy.org/databases/prosite/)).
* **Generation/Processing Date:** *("2023-03-18")*
* **Processing Steps:** Raw output from ps_scan.
* **Original Licensing:** PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License.