YGOB statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

YGOB specifications

Information


Unique identifier OMICS_03114
Name YGOB
Alternative name Yeast Gene Order Browser
Restrictions to use None
Maintained Yes

Publication for Yeast Gene Order Browser

YGOB citations

 (37)
library_books

Evolutionary instability of CUG Leu in the genetic code of budding yeasts

2018
Nat Commun
PMCID: 5951914
PMID: 29760453
DOI: 10.1038/s41467-018-04374-7

[…] next) as potential genes, provided that they were ≥180 bp long and did not overlap by >50 bp with a longer ORF. ORFs were translated using the standard genetic code and searched by BLASTP against the Yeast Gene Order Browser database of proteins with a cutoff of E ≤ 1e−10. The set of BLAST high-scoring pairs (HSPs) from a genome was then processed to populate a matrix of 64 codons × 20 amino acids […]

library_books

Gene regulation in Kluyveromyces marxianus in the context of chromosomes

2018
PLoS One
PMCID: 5773181
PMID: 29346402
DOI: 10.1371/journal.pone.0190913

[…] ning INU1 is found. The closest match to the gene product of INU1 of K. marxianus in S. cerevisiae was the invertase encoded by SUC2. In S. cerevisiae, SUC2 is found on chromosome IX (Fig F in ). The Yeast Gene Order Browser [] is a useful tool to investigate synteny among regions on yeast genomes. Fig G in shows that GIP1, ZTA1 and FMP23 are conserved in a region of synteny in all pre-genome dup […]

call_split

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

2017
Sci Rep
PMCID: 5680185
PMID: 29123238
DOI: 10.1038/s41598-017-15484-5
call_split See protocol

[…] red each single gene as a genome marker, and used distinct integers to represent the homologous genes across different yeast species. The yeasts homologous genes were defined by the original database YGOB, which was based on the BDBH BLASTP (E < 1e−5) using L. waltii and S. cerevisiae as reference genomes. Each group of homologous genes was represented by a specific gene order, no matter how many […]

library_books

A Comprehensive Analysis of Transcript Supported De Novo Genes in Saccharomyces sensu stricto Yeasts

2017
Mol Biol Evol
PMCID: 5850716
PMID: 28981695
DOI: 10.1093/molbev/msx210

[…] Genome sequence and ortholog assignment data of 21 Saccharomycetaceae species were obtained from the YGOB data set (). Synteny information was obtained from a previous study (step 5 in ) (). For candidate genes overlapping with ScANCs, 3 kb-proximal regions of ScANCs were considered as syntenic seque […]

library_books

Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole genome duplication after a failed mating type switch

2017
PLoS Biol
PMCID: 5433688
PMID: 28510588
DOI: 10.1371/journal.pbio.2002128

[…] the status of rearrangement points and pseudogenes discussed in the text.The Z. parabailii chromosomes were annotated using an improved version of our automated YGAP [], which uses information in the Yeast Gene Order Browser [] and the Ancestral (pre-WGD) gene order [] to generate a synteny-based annotation. The automated annotation was curated using transcriptome data from ATCC60483 cultures grow […]

library_books

Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments

2017
PLoS Genet
PMCID: 5409178
PMID: 28410373
DOI: 10.1371/journal.pgen.1006735

[…] Protein sequences used for the comparative analyses were from the Yeast Gene Order Browser []. These proteins were then aligned with MAFFT []. Genomic sequences for BY4741 and BY4742 were obtained from the Saccharomyces Genome Database [].To perform our comparative […]

Citations

Looking to check out a full list of citations?

YGOB institution(s)
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin, Ireland

YGOB reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review YGOB