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Table 5 A suite of programs to identify synteny blocks

From: Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

Step

Step designation

Tool

Reference

1

Identifying homologs

Darwin AllAll

Gonnet et al., 1992

2a

Identifying orthologs by RSD

Perl script rsd_ortho

FL, this work

2b

Clustering homologs

Perl script famtrans

FL, this work

2c

Breaking bridges

Graph algorithm (Perl graph library) cutbridge

FL, this work

2d

Extracting significant clusters

MCL algorithm

van Dongen, 2000

2e

Identifying orthologs in evolutionary trees

Perl script tree_ortho

FL, this work

3a

Identifying pairs of adjacent orthologous genes

Querying PostgreSQL database SynteBase

FL, this work

3b

Finding out synteny blocks

Perl script synblock

FL, this work