From gilbertd from net.bio.net  Wed Sep  1 22:59:13 2010
From: gilbertd from net.bio.net (Don Gilbert)
Date: Wed Sep  1 23:01:03 2010
Subject: [Arthropod] Ant genomes paper is public
Message-ID: <201009020359.o823xDM03869@net.bio.net>


This report on two ant genomes is recently published
http://www.sciencemag.org/cgi/content/abstract/329/5995/1068
DOI: 10.1126/science.1192428
Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator
...
I've not read this in detail but at a glance these genomes appear
to be like the 2 other hymenopera. The genome contig sequence are
available in the WGS section at NCBI: 26,840 contigs for
Harpegnathos, 32,174 for Camponotus.  I don't know if higher assemblies
or gene models are publicly available.

- Don Gilbert

From jyang29 from emory.edu  Wed Sep  8 16:27:51 2010
From: jyang29 from emory.edu (jyang29)
Date: Wed Sep  8 16:48:11 2010
Subject: [Arthropod] question about DroSpeGe
In-Reply-To: <20100908171636.47186du35tpc9zqs@webmail.service.emory.edu>
References: <20100908171636.47186du35tpc9zqs@webmail.service.emory.edu>
Message-ID: <20100908172751.119016znjzp8fzyv@webmail.service.emory.edu>

Dear Sir,

I want to use the table of synteny-data from DroSpeGe. I have a few questions.

1. Are the genomes used for synteny creation all the most updated ones?

2. When you said large scale synteny, what do you mean? What is the  
threshold of the size?

3. I want a table for the conserved region for any Drosophila species  
pair, do you have any suggestion for how I can get this information?

Regards,

JP




From gilbertd from cricket.bio.indiana.edu  Thu Sep  9 21:23:43 2010
From: gilbertd from cricket.bio.indiana.edu (Don Gilbert)
Date: Thu Sep  9 21:24:37 2010
Subject: [Arthropod] question about DroSpeGe
Message-ID: <201009100223.o8A2Nht18904@cricket.bio.indiana.edu>


JP,

You are refering to my work done 4 years back on this document
http://insects.eugenes.org/species/maps/muller-elements/
for the 12 drosophila genomes project.  I am not now updating DroSpeGe
data, as the genomes have been published for a while and are in
others' hands for work. It may be that I will update parts in the
future for DroSpeGe if someone has a good idea and wants my collaboration.
For instance, find there recent work of mine with Rnaseq used for 
gene prediction with Dros. data from the modEncode project.

For the synteny maps at above, "large scale" means syntenic regions
big enough to see on those tiny image maps, for 20Mb - 30Mb chromosomes,
so these are on the order of 500Kb - 1Mb (i.e. not microsynteny).
The software I used is linked on the above page, as is the data
(basic blast between species chromosome assemblies).

I don't know what versions of Drosophila the UCSC genome project has now,
but they make cross-species sequence conservation tables available.

- Don Gilbert

From dmerrill from ksu.edu  Thu Sep 16 11:02:52 2010
From: dmerrill from ksu.edu (Doris Merrill)
Date: Thu Sep 16 13:33:08 2010
Subject: [Arthropod] ARTHROPOD GENOMICS SYMPOSIUM, June 9-12, 2011,
	in Kansas City
Message-ID: <84CCC8EAC4024F4DB3782B989650017C@ecogenoffice>

ARTHROPOD GENOMICS SYMPOSIUM, June 9-12, 2011, in Kansas City

 

Please SAVE THE DATES of. 

June 9 to June 12

on your calendar and plan to attend the

5th ANNUAL ARTHROPOD GENOMICS SYMPOSIUM.

 

 

DATES:    June 9 to 12, 2011

PLACE:    Kansas City Marriott on the beautiful Country Club Plaza

SPONSOR:  K-State Arthropod Genomics Center, Kansas State University

TENTATIVE SCHEDULE:

   Thursday afternoon, June 9 - Pre-Symposium Workshop

   Thursday evening, June 9 - Keynote presentation and welcome reception

   Friday & Saturday, June 10 and 11 - Platform and Poster sessions 

   Sunday morning, June 12 - Roundtable discussion with 

         the ArthropodBase Consortium.  All are invited to attend!  

   Noon, Sunday, June 13 - Activities will conclude.

 

Speakers who are experts in arthropod genomics and bioinformatics with
applications in genomics will be announced soon!  Additional speakers will
be selected from contributed posters. 

 

Demonstrations: Database and bioinformatics tools developers will be
available at the meeting to provide hands-on demonstrations. 

 

Visit our website, www.k-state.edu/agc, for updates as details are
finalized.  We hope you will plan to attend!!!

 

Please help us "paperlessly publicize" the Symposium and share this
announcement with colleagues and students! 

 

 

Doris Merrill, Program Coordinator

K-State Arthropod Genomics Center

Division of Biology, Kansas State University

104 Ackert Hall, Manhattan, KS  66506-4901

(785) 532-3482, dmerrill@k-state.edu 

www.k-state.edu/agc