No functional descriptions available for the new models in any of the files I looked at. Sent email to authors:
to: huangsanwen@caas.cn, doug@qgg.au.dk, zhiwu.zhang@wsu.edu, shizhong.xu@ucr.edu, thomas.staedler@usys.ethz.ch, zf25@cornell.edu,
cc: RobertReid@uncc.edu, nfreese@uncc.edu, zhouyao@caas.cn, zhangzhiyangcs@163.com, baozhigui@caas.cn
Dear Drs. Huang, Speed, Xu, Städler, Fei, Mueller, and Zhang,
Congratulations on your new publication "Graph pangenome captures missing heritability and empowers tomato breeding."
I am very excited to use your new reference assembly (SL5.0) in my RNA-Seq data analysis projects!
I am writing to ask your help:
I am looking for the Gene Ontology annotations mentioned in the article, and also for human-friend text descriptions of the new gene models, if available.
I looked on the Sol Genomics Web site and in the Supplemental Data files available from the journal Web site, but could not find any GO annotations or text descriptions of each gene (or mRNA transcript).
Would you be able to send these to me?
The text descriptions of gene models would be especially valuable for interpreting results from RNA-Seq and other experiments that produce big lists of "significant" genes.
If you can provide descriptions for each model, I could include them in Integrated Genome Browser, a software tool my lab develops (https://bioviz.org). This software lets users quickly explore and analyze data from RNA-Seq, Chip-Seq and other genome-focused experiments.
In IGB, if a user clicks on a gene model, they can see a text description of the gene model, if the annotation provider (yourself) has provided this.
Users can even do keyword searches of the descriptions, as shown in the attached screen capture image from SL4.0. Including a short description of each gene model makes it much easier to understand and explore the results from RNA-Seq and other similar experiments.
So, I hope you will be able to provide both a short text description for each gene model, along with the Gene Ontology annotations!
Warm regards,
Ann Loraine, Ph.D.
Professor, Bioinformatics & Genomics
Genome Visualization Lab
College of Computing & Informatics
University of North Carolina, Charlotte
https://lorainelab.org
https://bioviz.org
Reply from Yao Zhou:
Dear Ann,
We now released the GO annotation of SL5.0 in our website (http://solomics.agis.org.cn/tomato/ftp/GO/). Unfortunately, we do not have a text descriptions of the new gene models.
Naama, would you please help us upload the GO annotation to SGN website? Thanks!
Best regards,
Yao
Obtaining copy of the IGB Quickload subversion repository with genome sequences and annotations, after installing subversion using "homebrew" on my Apple.
Command to checkout the repository is:
svn --username=aloraine co https://svn.bioviz.org/repos/genomes/quickload