<div dir="ltr"><div>Hi Shu,<br><br>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 <a href="http://archive.gramene.org/protein/">http://archive.gramene.org/protein/</a><br>
<br></div>Marcela<br><div><br><div class="gmail_extra"><br clear="all"><br><br><div class="gmail_quote">On Fri, Mar 28, 2014 at 11:34 AM, Shu CHEN <span dir="ltr"><<a href="mailto:szc0049@tigermail.auburn.edu" target="_blank">szc0049@tigermail.auburn.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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:<br>
<br>
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:// <a href="http://www.ncbi.nlm.nih.gov" target="_blank">www.ncbi.nlm.nih.gov</a>; verifi ed 19 July 2010), sorghum from JGI (<a href="http://www.jgi.doe.gov/" target="_blank">http://www.jgi.doe.gov/</a>; verifi ed 19 July 2010), and Poaceae from Gramene (<a href="http://www.gramene.org" target="_blank">http://www.gramene.org</a>; veri- fi ed 19 July 2010).<br>
<br>
<br>
Shu Chen<br>
<br>
Ph.D. Student<br>
<br>
Department of Agronomy and Soils<br>
<br>
RM 165, Funchess Hall<br>
<br>
________________________________<br>
发件人: <a href="mailto:mkmonaco.cshl@gmail.com">mkmonaco.cshl@gmail.com</a> <<a href="mailto:mkmonaco.cshl@gmail.com">mkmonaco.cshl@gmail.com</a>> 代表 Marcela K. Monaco <<a href="mailto:mmonaco@cshl.edu">mmonaco@cshl.edu</a>><br>
发送时间: 2014年3月28日 15:29<br>
收件人: Shu CHEN<br>
抄送: <a href="mailto:feedback@gramene.org">feedback@gramene.org</a><br>
主题: Re: [Feedback] [Website feedback] About the database Poaceae<br>
<br>
Hello Shu,<br>
<br>
The sentence simply refers to our own proteins database (data currently only accessible via our archives at <a href="http://archive.gramene.org/protein" target="_blank">http://archive.gramene.org/protein</a> page). 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).<br>
<br>
Hope this helps,<br>
<br>
Marcela<br>
<br>
==<br>
Marcela Karey Monaco, PhD<br>
Gramene Project Coordinator<br>
Cold Spring Harbor Laboratory<br>
One Bungtown Road, Williams #5<br>
Cold Spring Harbor, NY 11724<br>
Phone: <a href="tel:516-367-8808" value="+15163678808">516-367-8808</a><br>
Fax: <a href="tel:516-367-6851" value="+15163676851">516-367-6851</a><br>
<br>
<br>
On Thu, Mar 27, 2014 at 6:01 PM, <a href="mailto:szc0049@auburn.edu">szc0049@auburn.edu</a><mailto:<a href="mailto:szc0049@auburn.edu">szc0049@auburn.edu</a>> <<a href="mailto:szc0049@auburn.edu">szc0049@auburn.edu</a><mailto:<a href="mailto:szc0049@auburn.edu">szc0049@auburn.edu</a>>> wrote:<br>
shu (<a href="mailto:szc0049@auburn.edu">szc0049@auburn.edu</a><mailto:<a href="mailto:szc0049@auburn.edu">szc0049@auburn.edu</a>>) sent a message using the contact form at<br>
<a href="http://www.gramene.org/contact" target="_blank">http://www.gramene.org/contact</a>.<br>
<br>
I read some paper using a database called Poaceae in your website<br>
(Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic<br>
Biomass Crop).<br>
But I am having trouble finding this database. In your FTP serve, I can only<br>
find files for specific species.<br>
I did find a link here <a href="http://archive.gramene.org/protein/" target="_blank">http://archive.gramene.org/protein/</a>, in the sentence<br>
'The Protein Database at Gramene provides collective information on<br>
Swissprot-Trembl protein entries from family Poaceae (Grasses).' . It seems<br>
that Poaceae is linked to somewhere, but the page is no longer available.<br>
<br>
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</blockquote></div><br></div></div></div>