View source for SGD Newsletter, Spring 2021

[[Category:Newsletter]]
'''About this newsletter:''' <br>

This is the Summer 2021 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 also subscribe to SGD's RSS feed to receive updates on SGD news:
http://www.yeastgenome.org/feed<br>

==R64.3 Annotation Update==
SGD curators periodically update the chromosomal annotations of the ''S. cerevisiae'' Reference Genome, which is derived from strain [http://www.yeastgenome.org/strain/S288C/overview S288C].

The R64.3 annotation release included various updates and additions:

*7 new ORFs: [https://www.yeastgenome.org/locus/S000303806 OTO1/YGR227C-A], [https://www.yeastgenome.org/locus/S000303807 YHR052C-B], [https://www.yeastgenome.org/locus/S000303808 YHR054C-B], [https://www.yeastgenome.org/locus/S000303810 YJR107C-A], [https://www.yeastgenome.org/locus/S000303811 YKL104W-A], [https://www.yeastgenome.org/locus/S000303812 YLR379W-A], [https://www.yeastgenome.org/locus/S000303813 YMR008C-A]
*5 new ncRNAs: [https://www.yeastgenome.org/locus/S000303802 GAL10-ncRNA], [https://www.yeastgenome.org/locus/S000303803 TBRT/XUT_2F-154], [https://www.yeastgenome.org/locus/S000303809 SUT169], [https://www.yeastgenome.org/locus/S000303814 PHO84 lncRNA], [https://www.yeastgenome.org/locus/S000303815 GAL4 lncRNA]
*2 new uORFs for [https://www.yeastgenome.org/locus/S000003139 ROK1/YGL171W]
*1 new recombination enhancer: [https://www.yeastgenome.org/locus/S000303804 RE]
*1 new LTR: [https://www.yeastgenome.org/locus/S000303805 YELWdelta27]
*3 ORFs with shifted translation starts: [https://www.yeastgenome.org/locus/S000000792 HPA3/YEL066W], [https://www.yeastgenome.org/locus/S000003773 YJR012C], [https://www.yeastgenome.org/locus/S000005204 LTO1/YNL260C]
*1 ORF with shifted translation stop plus new intron: [https://www.yeastgenome.org/locus/S000004755 LDO45/YMR147W]
*Changed feature_type (and SO_term) for non-transcribed spacers: [https://www.yeastgenome.org/locus/S000029714 NTS1-2], [https://www.yeastgenome.org/locus/S000029329 NTS2-1], [https://www.yeastgenome.org/locus/S000029706 NTS2-2]
*New systematic nomenclature system for [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs]

Various sequence and annotation files are available on SGD's [http://sgd-archive.yeastgenome.org/sequence/S288C_reference/ Downloads] site. You can find more update details and see the new systematic nomenclature system for noncoding RNA genes on the [https://wiki.yeastgenome.org/index.php/Details_of_2021_Reference_Genome_Annotation_Update_R64.3#R64.3_Annotation_update_summary Details of 2021 Reference Genome Annotation Update R64.3] SGD Wiki page.

==Alliance Item==

==YeastMine Updates and New Templates==
[[File:ym_templates.png|400px|left|thumb|upright=0.8|Transcript and UTR YeastMine Templates]]
<br>SGD has updated the current [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_UTRs&scope=all Gene-->UTRs] template with newly calculated 5' and 3' UTR sequence/coordinates. Additionally, Transcript iso-forms for specific genes from the [http://www.yeastgenome.org/reference/S000153368/overview Pelachano et al 2013] study can be accessed in YeastMine using the new [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Transcript&scope=all Gene-->Transcript] template. Both templates can be found under the 'Templates' section of YeastMine under the 'Expression' category.
























==Textpresso Update==
[[File:textpresso.png|600px|thumb|left|upright=0.8|Textpresso Homepage]]
[https://textpresso.yeastgenome.org/tpc/home Textpresso] has recently been updated with a new system, bringing an overhauled user interface and new features. The updated Textpresso still allows users to search the corpus of texts with specialized queries using keywords and related categories, but now search results are shown in the context of the full text. More information about the changes and types of papers stored in Textpresso can be found in their [https://textpresso.yeastgenome.org/tpc/aboutus About Us] help section.


























==Fungal Pathogen Genomics Workshop==
From May 10th - 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander attended the Fungal Pathogen Genomics Workshop. Our curators helped attendees learn more about using the unique tools on our website and were also able to interact with curators from other fungal databases at FungiDB, EnsemblFungi, PomBase, CGD, MycoCosm, and JGI. 

We would like to thank the Fungal Pathogen Genomics team for hosting a fun and successful virtual workshop for experimental biologists to gain valuable experience! 

[[File:workshop.png]]

==New Homology Pages==

SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.

insert picture later

The information displayed on the Homology Pages is divided into several sections:

*Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
*Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
*Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
*External Identifiers: A list of external identifiers for the protein from various database sources.

[[File:homology1.png|650px|left|Image: 650 pixels]] [[File:homology2.png|650px|Image: 650 pixels]]


















==Functional Complementation Data Available on References Pages==
Functional Complementation annotations are now viewable on reference pages for which there is curatable functional complementation data. This information describes cross-species functional complementation between yeast and other species, and is curated by SGD and the Princeton Protein Orthology Database (P-POD). 

insert picture

==More Alleles==
SGD now has approximately '''13,000''' alleles that are either fully or partially curated. You can generate a list of all alleles in our database using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Alleles&scope=all Genes --> Alleles] template in [https://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine], or search for a specific allele in the website search bar.

picture of search with allele count? allele page? no pic?