SGD Newsletter, Summer 2024 - Revision history

Stacia: /* Updates to SGD search */

2024-06-19T18:56:10Z

‎Updates to SGD search

Stacia: /* Upcoming conferences and courses */

2024-06-18T21:25:20Z

‎Upcoming conferences and courses

Stacia: /* Extended gene coordinates in GFF */

2024-06-18T21:18:52Z

‎Extended gene coordinates in GFF

Stacia: /* Extended gene coordinates in GFF */

2024-06-18T21:18:38Z

‎Extended gene coordinates in GFF

Stacia: /* Extended gene coordinates in GFF */

2024-06-18T21:18:25Z

‎Extended gene coordinates in GFF

Stacia: /* Extended gene coordinates in GFF */

2024-06-18T21:18:05Z

‎Extended gene coordinates in GFF

Stacia: /* Extended gene coordinates in GFF */

2024-06-18T21:17:40Z

‎Extended gene coordinates in GFF

Stacia: /* Extended gene coordinates in GFF */

2024-06-18T21:17:19Z

‎Extended gene coordinates in GFF

Stacia: /* Extended gene coordinates in GFF */

2024-06-18T21:10:46Z

‎Extended gene coordinates in GFF

Stacia: /* Extended gene coordinates in GFF */

2024-06-18T21:09:37Z

‎Extended gene coordinates in GFF

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 *New category for [https://www.yeastgenome.org/search?q=&category=dataset datasets]. Over 3700 yeast datasets are accessible. Search by reference, keyword, assay, and lab.
 *Macromolecular [https://www.yeastgenome.org/search?q=&category=complex complexes] can now be searched with aliases. Further refine by reference, subunit, function, process, and location.
 *Search for [https://www.yeastgenome.org/search?q=&category=allele alleles] via their descriptions and SGDIDs. Drill down based on reference, allele type, gene, and phenotype.

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 **June 24 to June 27, 2024
 **Montanya Hotel & Lodge, Catalonia, Spain
 *[https://www.pnwyc.net Pacific Northwest Yeast Club]
 **July 26, 2024

@@ Line 38: / Line 38: @@
 In recent years, SGD has made two significant changes to the GFF content (described in more detail below):
-*In November 2020, we updated the file to reflect experimentally determined transcripts
+*In November 2020, SGD updated the file to reflect experimentally determined transcripts
-*In February 2024, we edited the 'gene' entries in the file to extend the coordinates to encompass the start and stop coordinates of the longest experimentally determined transcripts
+*In February 2024, SGD edited the 'gene' entries in the file to extend the coordinates to encompass the start and stop coordinates of the longest experimentally determined transcripts
 In 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.

@@ Line 38: / Line 38: @@
 In recent years, SGD has made two significant changes to the GFF content (described in more detail below):
-*In November 2020, SGD updated the file to reflect experimentally determined transcripts
+*In November 2020, we updated the file to reflect experimentally determined transcripts
-*In February 2024, SGD edited the 'gene' entries in the file to extend the coordinates to encompass the start and stop coordinates of the longest experimentally determined transcripts
+*In February 2024, we edited the 'gene' entries in the file to extend the coordinates to encompass the start and stop coordinates of the longest experimentally determined transcripts
 In 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.

@@ Line 39: / Line 39: @@
 In recent years, SGD has made two significant changes to the GFF content (described in more detail below):
 *In November 2020, SGD updated the file to reflect experimentally determined transcripts
-*In February 2024, SGD edited the 'gene' entries in the file to extend the coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts
+*In February 2024, SGD edited the 'gene' entries in the file to extend the coordinates to encompass the start and stop coordinates of the longest experimentally determined transcripts
 In 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.

@@ Line 37: / Line 37: @@
 The saccharomyces_cerevisiae.gff contains sequence features of ''Saccharomyces cerevisiae'' and related information such as Locus descriptions and GO annotations. The saccharomyces_cerevisiae.gff is fully compatible with [http://gmod.org/wiki/GFF3 Generic Feature Format Version 3], and is [http://sgd-archive.yeastgenome.org/curation/chromosomal_feature/ updated weekly].
-*In 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.
+In recent years, SGD has made two significant changes to the GFF content (described in more detail below):
 ''Starting November 2020: BDH2/YAL061W with rows for longest transcripts expressed in GAL and in YPD.''
 [[File:yal061w_w2transcripts.jpg]]
-*Then 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).
+Then 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 expanded start/stop coordinates for 'gene', still with rows for longest transcripts expressed in GAL, YPD.''