From: SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes
Step | Step designation | Tool | Reference |
---|---|---|---|
1 | identifying homologues | protein Blast | [22] |
2a | identifying orthologues by RBH | Perl script rsd ortho | FL, this work |
2b | clustering homologues | Perl script famtrans | FL, this work |
2c | breaking bridges | graph algorithm (Perl library) | FL, this work |
2d | extracting significant clusters | MCL algorithm | [23] |
3a | identifying pairs of adjacent orthologous genes | SQL query on SynteBase | FL, this work |
3b | discovering synteny blocks | Perl script synblock | FL, this work |