To construct the PlantPathMarks (PPMdb) core database, we integrated two powerful tools called MISA (MIcroSAtellite identification) and primer3 into our in-house-developed “Perl and Shell” scripts to strap all standalone bioinformatic analysis steps in one main pipeline called Pathway Gene-Set Mining (PGM) pipeline. This pipeline was built to develop two novel marker systems called Pathway Genes-Targeted Markers (PGTM) and Pathway Microsatellites-Targeted Markers (PMTM). This pipeline was implemented to construct our PPMdb sub-databases through seven main steps, as follows: (a) splitting the retrieved genomic data into sequence and annotation files (b) classifying genomic sequence into genic or intergenic (c) sub-classifying genes into enzyme- coding or non-enzyme-coding (d) mining microsatellites on enzyme-coding genes only (this step exclusive to PMTM) (e) designing primers and classifying markers into PMTM or PGTM (f) mapping all designed primers against KEGG reference maps.
**Shell Files
- Shell_step1.sh
- misa.sh
- Extract-seq.sh
- Extract-seq_EST.sh
- PGTM_primers.sh
- PPTM_primers.sh
- map_primers_KEGG_Maps.sh
**Perl scripts (Folder Script/)
- Etract-Feature.pl
- multigb_to_multifasta.pl
- extractseq.pl
- misa.pl
- p3_in.pl
- p3_in2.pl
- p3_out.pl
For questions and Issues please contact: morad.mokhtar@ageri.sci.eg; morad.mokhtar@um6p.ma
Citations
If you find this scripts useful, please cite:
Morad M. Mokhtar, Achraf El Allali, Mohamed-Elamir F. Hegazy & Mohamed A. M. Atia. PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes. Scientific Reports 11, 21300 (2021). https://doi.org/10.1038/s41598-021-00504-2