How to usefully compare homologous plant genes and chromosomes as DNA sequences.
By E. Lyons, Michael Freeling. The Plant Journal, 2008
480 citations recorded by the source corpus.
Subfields: Genetics, Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/18c383f95559ec3798d0298df0a84505d4650e33
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Citations in the corpus
- Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing. (2017, methodology): “…SOURCE IDENTIFIER Custom Perl script for off-target sites search This study NA SeqMan DNASTAR Lasergene http://www.dnastar.com CoGe Gevo tool (Lyons and Freeling, 2008) https://www.genomevolution.org/coge/ mVISTA (Mathelier et al., 2014) http://genome.lbl.gov/vista/mvista/about.shtml JASPAR…”
- Phylogenetic distribution of three pathways for propionate production within the human gut microbiota (2014, methodology): “…designed by visual inspection of protein sequence alignments of genes detected by blastp analysis (Altschul et al., 1990) against the non-redundant database at NCBI (http://blast.ncbi. nlm.nih.gov/Blast.cgi) and using the CoGe database (http://genomevolution.org/CoGe/) (Lyons and Freeling, 2008).”
- PGDD: a database of gene and genome duplication in plants (2012, methodology): “Besides developing the OpenAPI and RESTful web services, we plan to develop interfaces to link multiple data sources such as the VISTA (55) suite of programs and databases for multi-way analysis of genomic sequences, and CoGe (22), web application to display the homologous regions across multiple ge”
- Locating rearrangement events in a phylogeny based on highly fragmented assemblies (2016, background): “A set of five or ten genes in the same order, with few intervening genes, in two genomes can be confidently identified as a conserved syntenic block [5, 6].”
- Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. (2009, background): “pl), part of the CoGe suite of comparative genomics research applications (61), to prepare this alignment between part of Arabidopsis chromosome 3 and part of chromosome 5.”