#150: sequence to GV
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Reporter: liste | Owner: thabe
Type: enhancement | Status: new
Priority: major | Milestone: BOGAS_v4
Component: ArteminiServices | Version:
Keywords: |
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need a diff system of getting seq to GV (art??), because loading full
chrom of Medtr already is difficult.
save will also not work due to server upload file limit
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Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/150>
BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas>
Bioinformatics Online Genome Annotation Service
#161: prot DOM section and figure
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Reporter: liste | Owner: liste
Type: task | Status: new
Priority: major | Milestone: BOGAS_v4
Component: Website | Version:
Keywords: |
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check section + fig to see if multiple occurrences of the same domain is
available.
(if map to hash -> no, replace by array or so)
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Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/161>
BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas>
Bioinformatics Online Genome Annotation Service
dear colleague
can I get a username to connect at
http://bioinformatics.psb.ugent.be/webtools/bogas/
<http://bioinformatics.psb.ugent.be/webtools/bogas/%29%C2%A0>
thanks
christophe
Le 23/01/2012 19:24, Zander Myburg a écrit :
> Dear EUCAGEN members and genome paper collaborators,
> This is a quick update on the status of the DOE-JGI /E. grandis
> /genome project and the associated genome paper. There has been some
> important developments that will affect the genome analysis, the
> schedule of the genome paper and the content of companion papers.
> **
> *UPDATED ANNOTATION (V1.1)*
> The JGI has produced a new filtered annotation set (V1.1) of the
> initial 8X mapped /Eucalyptus grandis BRASUZ1/ genome assembly. This
> version (1.1) is a subset of the initial annotation (1.0) and was
> released together with Phytozome 8.0 (Jan 16, 2012). V1.1 was produced
> by filtering (out) 8620 low-confidence gene models from the original
> v1.0 annotation using criteria described on Phytozome
> http://www.phytozome.net/eucalyptus.php. Most of the removed gene
> models are short, incomplete models with little or no EST support and
> most form singletons in the Phytozome gene cluster database (i.e. they
> do not cluster with any other known proteins). In short, we consider
> this subset (36,376 primary protein coding loci) a high confidence
> subset and will report it as such in the main genome paper. Some
> contributors have already indicated that they have expression evidence
> for some removed gene models, or that they can find full length
> versions of the gene models using their own gene predictions. It is
> therefore likely that some legitimate gene models are included in the
> filtered set, which is why V1.0 will still be available in Phytozome
> (browser track and searchable). My opinion is that the filtered set is
> an important part of the genome biology of Eucalyptus - we see many
> pseudogenes and it is possible that the genome is undergoing gene loss
> after whole-genome duplication and high rates of tandem duplication.
> The V1.1 annotation files are available for download at
> ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Egrandis/annotation/. The
> low confidence, filtered set is also available for download there.
> We have decided to report gene numbers for the initial V1.0 annotation
> in the main genome paper and to report the V1.1 subset as a "high
> confidence" subset. This means that collaborators working on companion
> papers can keep V1.0 models in figures and tables, and then provide
> summary data for the high confidence models in their papers and
> supplementary materials as needed. We would like people to rather
> highlight the high confidence subset rather than the low confidence
> filtered set.
> *GENOME PAPER DRAFT*
> I am at JGI this week working with Jerry Tuskan on the first full
> draft of the main genome paper. By the end of the week, we will have a
> much better idea of which contributed analyses, figures and tables can
> be included. Some of the analyses done for the genome paper (e.g.
> whole-genome duplication analysis) will have to be rerun with V1.1. We
> will contact people directly for updated results. In some cases we
> also need both a short and a detailed version of the methods used to
> produce the contributed results (for the Online Methods and
> Supplementary Notes sections of the paper). We will contact people
> directly for that. Please be ready to provide updated results (v1.1
> numbers) and methods for the genome paper draft. At this stage we are
> looking at producing a final draft by end of March/early April and
> will circulate the first draft to core collaborators as soon as possible.
> *COMPANION PAPERS*
> We have a list of draft companion paper abstracts that we will use to
> motivate a special issue of New Phytologist. If anybody wants to
> submit additional abstracts for consideration, those can be emailed to
> me by the end of this week. An updated list of submitted abstracts
> will be uploaded to the Eucalyptus Genome Wiki on
> BOGAS (http://bioinformatics.psb.ugent.be/webtools/bogas/)
> <http://bioinformatics.psb.ugent.be/webtools/bogas/%29%A0> At this
> stage, we would like companion papers to be in final draft by mid
> April. Papers that do not get included in the New Phytologist special
> issue can be submitted in other relevant journals such as BMG Genomics
> and Tree Genetics and Genomes.
> *E. CAMALDULENSIS GENOME*
> KASUZA DNA Research Institute in Japan has decided to release the E.
> camaldulensis genome sequence data which they have produced via the
> genome database on Kazusa DNA Inst website,
> http://www.kazusa.or.jp/eucaly/. Details of the database construction
> will be published on the Japanese Society for Plant Cell and Molecular
> Biology website http://www.jspcmb.jp/english/pbcontents/index.html. We
> are delighted about this development. The E. camaldulensis genome
> data, together with the E. globulus genome data produced by JGI and by
> collaborators in Australia will be very valuable for comparative
> genomics among these three representatives of the main sections of the
> subgenus Synphyomyrtus including most of the commercially grown
> eucalypts. We encourage collaborators to make use of the E.
> camaldulensis genome resource.
> I hope that you find this information useful. Please email me if you
> have any questions or suggestions for the main genome paper or
> companion papers.
> Kind regards
> Zander Myburg
> **
>
>
> >>>
> *From: * "David M. Goodstein" <dmgoodstein(a)lbl.gov>
> *To:* <phytozome-user(a)lists.lbl.gov>
> *Date: * 2012/01/17 01:51 PM
> *Subject: * Announcing the release of Phytozome v8.0
>
> Highlights include:
>
> *JGI Genomes:*
> -preliminary assembly and annotation of */Panicum virgatum/*
> (switchgrass) and */Phaseolus vulgaris/* (common bean)
> -assembly and annotation of the arabidopsis comparator */Capsella
> rubella/*
> -Updated annotations of /*Aquilegia coerulea*, *Eucalyptus grandis*/,
> and */Volvox carteri/*
> *
> *
> *External Genomes:*
> *-*updated annotations of /*Brachypodium distachyon*/, /*Oryza
> sativa*/ (rice), /*Zea mays* /(maize)
> -addition of */Linum usitatissimum/ *(flax), /*Brassica rapa*/ (napa
> cabbage), */Malus domestica/ *(apple).
>
>
> regards,
>
> The JGI Phytozome Team
>
>
>
>
>
>
>
>
>
>
>
>
#184: genome / annotation stats summary table
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Reporter: brhel | Owner: liste
Type: enhancement | Status: new
Priority: major | Milestone:
Component: Website | Version:
Keywords: |
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A table describing some genome / annotation statistics. This table should
be updated using a script (and not after each gene update, as it might hog
resources on large genomes).
I will come up with a Proposal involving a script to generate the stats +
a MySQL table structure to store this data.
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Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/184>
BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas>
Bioinformatics Online Genome Annotation Service
