Difference between revisions of "SGD Newsletter, Summer 2024"
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Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023). | Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023). | ||
| − | + | [[File:yal061w_extendedgene.jpg]] | |
| − | + | ''After February 2024: BDH2/YAL061W with increased start/stop coordinates.'' | |
| − | After February 2024: BDH2/YAL061W with increased start/stop coordinates. | ||
This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource. | This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource. | ||
Revision as of 15:43, 11 June 2024
About this newsletter:
This is the Summer 2024 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this newsletter as well as previous newsletters, on the SGD Community Wiki.
Contents
Ref genome update R64.5
Extend gene coordinates in GFF
The saccharomyces_cerevisiae.gff contains sequence features of Saccharomyces cerevisiae and related information such as Locus descriptions and GO annotations. It is fully compatible with Generic Feature Format Version 3. It is updated weekly.
After November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.
Old version: BDH2/YAL061W with longest transcripts expressed in GAL and in YPD.
Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).
After February 2024: BDH2/YAL061W with increased start/stop coordinates.
This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.
Updates to SGD search
datasets complex aliases allele descriptions, SGDIDs RNAcentral IDs
PubTator link on SGD reference pages
microPublications - latest yeast papers
Alliance of Genome Resources - Release x.x
AllianceMine link in black toolbar - ‘Get Data’
