[Feedback] 答复: [Website feedback] About the database Poaceae

[Marcela K. Monaco]

Hi Shu,

The sentence about Gramene in the referenced paper is not grammatically
correct, but I believe that the authors simply referred to the protein
database for species in the Poaceae plant family available in Gramene.
Protein data is still available from our legacy archives at
http://archive.gramene.org/protein/

Marcela




On Fri, Mar 28, 2014 at 11:34 AM, Shu CHEN <szc0049 at tigermail.auburn.edu>wrote:

> So there is not a collective protein database for all Poaceae species
> available in Gramene? I am just confused that the database was mentioned in
> the paper 'Investigation of the Transcriptome of Prairie Cord Grass, a New
> Cellulosic Biomass Crop', described as following:
>
> BLAST (Altschul et al., 1990) analyses of contigs and singlets derived
> from the assembly were conducted against six protein databases:
> non-redundant proteins, switchgrass, sugarcane (including Saccharum offi
> cinarum and Saccharum hybrid cultivar), maize from NCBI (http://
> www.ncbi.nlm.nih.gov; verifi ed 19 July 2010), sorghum from JGI (
> http://www.jgi.doe.gov/; verifi ed 19 July 2010), and Poaceae from
> Gramene (http://www.gramene.org; veri- fi ed 19 July 2010).​
>
>
> Shu Chen
>
> Ph.D. Student
>
> Department of Agronomy and Soils
>
> RM 165, Funchess Hall
>
> ________________________________
> 发件人: mkmonaco.cshl at gmail.com <mkmonaco.cshl at gmail.com> 代表 Marcela K.
> Monaco <mmonaco at cshl.edu>
> 发送时间: 2014年3月28日 15:29
> 收件人: Shu CHEN
> 抄送: feedback at gramene.org
> 主题: Re: [Feedback] [Website feedback] About the database Poaceae
>
> Hello Shu,
>
> The sentence simply refers to our own proteins database (data currently
> only accessible via our archives at http://archive.gramene.org/proteinpage).  Gramene is a database that initially focused on "true" grasses from
> the family Poaceae (Gramineae) including the monocot crops: rice, maize,
> sorghum, wheat, barley, etc.   But has now grown to include a range of
> species including a non-grass monocot crop: banana; dicot crops like
> soybean, tomato, potato, grape, etc; model organisms like Arabidopsis,
> Brachypodium, Medicago, etc.; and lower plants (green/blue algae, moss,
> etc).
>
> Hope this helps,
>
> Marcela
>
> ==
> Marcela Karey Monaco, PhD
> Gramene Project Coordinator
> Cold Spring Harbor Laboratory
> One Bungtown Road, Williams #5
> Cold Spring Harbor, NY 11724
> Phone: 516-367-8808
> Fax: 516-367-6851
>
>
> On Thu, Mar 27, 2014 at 6:01 PM, szc0049 at auburn.edu<mailto:
> szc0049 at auburn.edu> <szc0049 at auburn.edu<mailto:szc0049 at auburn.edu>> wrote:
> shu (szc0049 at auburn.edu<mailto:szc0049 at auburn.edu>) sent a message using
> the contact form at
> http://www.gramene.org/contact.
>
> I read some paper using a database called Poaceae in your website
> (Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic
> Biomass Crop).
> But I am having trouble finding this database. In your FTP serve, I can
> only
> find files for specific species.
> I did find a link here http://archive.gramene.org/protein/, in the
> sentence
> 'The Protein Database at Gramene provides collective information on
> Swissprot-Trembl protein entries from family Poaceae (Grasses).' . It seems
> that Poaceae is linked to somewhere, but the page is no longer available.
>
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>
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