References

Here you can find a list of references to be cited whenever using a CoGe tool.

CoGe References

• Lyons E, Freeling M (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences. The Plant Journal 53:661-673
• Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D. (2008) Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids, Plant Phys 148, pp. 1772–1781.

Tools Used in CoGe

Tool	Reference
BLAST	Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215:403-410
BlastZ	Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W (2003) Human-mouse alignments with BLASTZ. Genome Research 13:103-7
DAGChainer	Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20: 3643–3646
QuotaAlign	Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M (2011) Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics DOI: 10.1186/1471-2105-12-102
ClustalW	Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:4673-4680
CHAOS	Brudno M., Chapman M., Göttgens B., Batzoglou S., Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics. 2003;4:66
DIALIGN 2	Morgenstern, B. (1999). DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15: 211–218
JalView
NJPlot
CODEML	Yang Z (2007) PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution 24:1586-1591

Genomes Used in CoGe

Unfortunately, due to the large number of genomes currently stored in CoGe (currently over 6,600), we cannot list all the references here. However, we are currently working on a system to automate the production of citations for searches. In the meantime, we urge you to find these citations on your own if you are to publish work based on data obtained from these genomes in addition to citing CoGe.

For a non-exhaustive list of publications describing plant genomes, see this page.