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Table 1 A suite of programs to detect and identify synteny blocks

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