Monthly Archives: May 2011

Third International Course in Automated Functional Annotation and Data Mining

I know of many researchers using next-generation sequencing techniques – from RNA-Seq and EST sequencing to shot-gun genome sequencing.  One of the hurdles in using these techniques, at least for me, is functionally annotating a large number of sequences, some of which can be quite small in size.

The computer analysis platform Blast2GO has been used quite extensively by many researchers for sequence annotation.  There have been a few successful short courses sponsored by the Blast2GO production team and they have now announced the Third International Course in Automated Functional Annotation and Data Mining.  Two short courses for this year will be held at UC Davis (Davis, California, USA, July 26th to 28th) and at CIPF (Valencia, Spain, September 28th to 30th).  For more information and registration visit the course website.

PhenoDays 2011 International Symposium

Genomics is directly increasing the amount of information at the hands of agricultural crop breeders, but phenotyping has become the research bottleneck for phenotype to genotype associations.

In an effort to alleviate this bottleneck, a group of researchers has organized the PhenoDays 2011 International Symposium which will be held October 12th to 14th in Wageningen, The Netherlands.  Symposium presentation talks will be given by researchers from both institutional and academic plant breeding groups, as well as industry representatives from the seed production industry.  In addition, there will be plant phenotyping workshops.  See the symposium website for more information and registration.

Schatz Tree Genetics Colloquium: Genetics, Ecology, and Management of Walnuts & Butternut

The Schatz Tree Genetics Colloquium is a biennial meeting focusing on the genetics of trees.  The purpose of this colloquium series is to advance the knowledge of tree genetics, breeding, and ecology, with each biennial meeting focusing on a specific family, genus, or species of tree (s).

This year’s colloquium meeting is entitled: Genetics, Ecology, and Management of Walnuts and Butternut.  This meeting will be held at the beautiful locale of the Penn State Mont Alto campus, on July 11th and 12th, 2011.  Registration for the meeting is FREE, although there is a $20 cost for the closing banquet.  Advanced registration is required as there is no on-site registration for the meeting.  Deadline for registration is June 24th, 2011.

Jacques Monod Conference: Integrative Ecological Genomics

Ecological genomics is thriving as a discipline, evidenced by the number of research papers published in this area, and this is due to the large amounts of genomic data now available to researchers.  Information from individual genomes, “pan-genomes”, and large scale environmental genome sequencing is giving us a more complete picture of biological diversity.

Some of the top researchers in this newly emerging discipline will be speaking at the Jacques Monod Conference “Integrative Ecological Genomics.”  The meeting is held in Roscoff, Brittany, France.  Registration is by application (the submission deadline is June 20th 2011) and the number of attendees is capped at 115 people.  Information regarding the meeting and registration can be found here and here.

New Phytologist Bioenergy Trees Symposium Wrap-Up

I’m just returning from the New PhytologistBioenergy Trees” symposium, which just took place from May 17th to 19th at INRA in Nancy, Lorraine, France, and I am pleased to say was a very productive meeting.  Due to technical difficulties, I was not able to contribute to the online updates via Twitter, but if you’d like to follow the meeting developments you can read the Twitter feeds using the hashtag #26NPS or following @NewPhyt.

A RADical Way To Assemble A Genome

If you’ve ever assembled a genome, you know what I daunting task it is.  It’s quite literally like putting a huge extremely complex puzzle together, one where the pieces are extremely small, and doing this, of course, all with the use of a computer.  The worse case scenario is the assembly of eukaryotic genomes where the puzzle is large in size with possibly millions of pieces to assemble, and some of these pieces look exactly like the other pieces.  In this scenario, to develop an even remotely questionable assembly – one that may not be fully put together – it can take days to weeks of computational time on the fastest of multi-processor computers with plenty of memory (for keeping huge amounts of sequence data active).

In an attempt to ease the assembly of larger genomes – genomes larger than those your typical bacteria – a research group at the University of Oregon led by molecular biologist Eric Johnson has developed a technique, which they call restriction-site associated DNA markers, or ‘RAD’ for short, which aids in providing a clearer view of overlapping sequenced reads.  A patent has been filed for this technology.

A new paper authored by Etter et al., entitled “Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads” and recently published in the journal PLoS One, provides proof of technology of the RAD technique by identifying genomic differences in numerous isolated populations, those from freshwater and saltwater habitats, of the threespine stickleback fish (see figure below).

The RAD markers act as placeholders that can be used to identify a space portion of the genome.  By using these markers, the authors were able to piece together regions of close proximity.  This quickly provided larger contigs than without using the RAD marker method. The authors stress that this technique is best used when applied to organisms that do not have a close reference genome.  Two commentaries regarding this research are located here and here.

RECOMB Comparative Genomics Workshop

Sponsored by the journal BMC Bioinformatics, the RECOMB Comparative Genomics Workshop, held this year in Galway, Ireland, will focus on connecting mathematicians, computer programmers, and biologists who are interested in comparative genomics using computational methods.  Both invited and contributed talks will be published as a supplement in BMC Bioinformatics.  Registration and more information is located here.