Tool:Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes

Question

[wangdp123]

I would like to introduce a suite of tools that are dedicated to the detection and visualization of conserved gene pairs and gene clusters, which can be used to study the co-linear phenomenon in the gene unit in a wide range of applications for your genome relevant studies.

DLGP: http://www.nextgenbioinformatics.org/DLGP

This database includes 134 animal and plant nuclear genome data.

Reference: Dapeng Wang. DLGP: A database for lineage-conserved and lineage-specific gene pairs in animal and plant genomes. Biochemical and Biophysical Research Communications. 2015.

Plastid-LCGbase: http://www.nextgenbioinformatics.org/plastid-LCGbase

This database contains 470 plastid genomes, most of which chloroplast genomes.

Reference: Dapeng Wang and Jun Yu. Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs. Nucleic Acids Research (2014).

LCGserver: http://www.nextgenbioinformatics.org/LCGserver

This webserver works for exploring evolutionary dynamics of gene orders over diverse lineages with the input data from users.

Reference: Dapeng Wang and Jun Yu. LCGserver: A Webserver for Exploring Evolutionary Trajectory of Gene Orders in a Large Number of Genomes. OMICS: A Journal of Integrative Biology. 2015 Sep;19(9):574-7.

Should you have any questions when using these tools, please do not hesitate to contact me by [e-mail]

Dapeng