Abstract
Background: The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid
sequence homologies. However, these phylogenetic tree analyses are not suitable for those “non-traditional” gene
families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap
values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of
placement of those members in those nodes.
Results: We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions
surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs
between two genomic fragments to determine the relationship between two members in a gene family. The
colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history
can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced
and non-expert users with a user-friendly graphical-user interface. MicroSyn is available from: http://fcsb.njau.edu.
cn/microsyn/.
Conclusions: Case studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase
family in Populus trichocarpa were presented to show the utility of the software. The easy using of MicroSyn in
these examples suggests that the software is an additional valuable means to address the problem intrinsic in the
computational methods and sequence qualities themselves in gene family analysis.
