EMBnet News bulletin of 21 Dec 2006

Laurent Falquet Laurent.Falquet at unil.ch
Thu Dec 21 15:20:01 CET 2006


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* EMBnet News bulletin of 21-Dec-2006 *
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Dear Users,

Courses in 2007
---------------

We will organise several courses in 2007:

1) Lausanne Feb 19-23: Introduction to protein structure
2) Basel  Mar 5-9: Introduction to Biostatistics
3) Bern Aug 27-31: Motifs in DNA sequences
4) Lausanne Sep 3-7: Phylogeny and Evolution using Bioinformatics

1) Introduction to protein structure (LS)
Three-dimensional protein structures are key to a detailed 
understanding of the molecular basis of protein function. Combining 
sequence information with 3D structure gives insights for the 
development of effective rational strategies for experiments such as 
site directed mutagenesis, studies of disease related mutations, or 
the structure based design of specific inhibitors.
Registration opened until January 20th:
http://www.3eme-cycle.ch/biologie/pages/registration_generic.html
For more information please contact Dr. Vassilios Ioannidis
vassilios.ioannidis at isb-sib.ch

2) Introduction to Biostatistics (BS)
This beginner course will touch a large panel of biological problems requiring
statistical data analysis, i.e. not only Microarrays!
Knowledge of statistics (or R package) would be an asset to fully
benefit from this course.
Registration will be announced soon on 
http://www.ch.embnet.ogr/pages/courses.html
or contact course organiser Dr. Lorenza.Bordoli at isb-sib.ch
This course is organized with the support of the Swiss Committee for  
Molecular Biology (SKMB) (http://www.usgeb.ch/skmb.html).

3) Motifs in DNA sequences (BE)
The course will focus on Bionformatics resources for studying transcription
regulatory motifs and networks.
More details to come.
Registration will be announced on http://www.ch.embnet.ogr/pages/courses.html
or contact course organiser Dr. Lorenza.Bordoli at isb-sib.ch
This course is organized with the support of the Swiss Committee for  
Molecular Biology (SKMB) (http://www.usgeb.ch/skmb.html).

4) Phylogeny and Evolution using Bioinformatics (LS)
Analysing molecular data is now a major way to investigate the 
evolution of organisms, while evolutionary analysis is becoming an 
important step in the analysis of genes and proteins, notably in the 
context of comparative genomics. The course aims to make the students 
autonomous in all the steps to study the evolution of genes and 
proteins, from phylogeny to detecting selection. It will cover both 
fundamental notions, and the latest developments.
Course topics:
	*	- multiple sequence alignment and data selection
	*	- parsimony methods for phylogeny
	*	- evolutionary models and distance methods for phylogeny
	*	- likelihood and Bayesian methods for phylogeny
	*	- tests and support measures in phylogeny
	*	- drawing and reading trees
	*	- testing and using molecular clocks
	*	- detecting selection
	*	- reconstructing ancestral sequences
	*	-summary: which methods and which data for my question
Invited professors:
	*	- Prof. Joe Felsenstein, University of Washington, USA
	*	- Dr. Nicolas Galtier, CNRS Montpellier, France
	*	- Dr. Stephane Guindon, CNRS Montpellier, France

Registration opened until July 31st:
http://www.3eme-cycle.ch/biologie/pages/registration_generic.html
For more information please contact Dr. Vassilios Ioannidis
vassilios.ioannidis at isb-sib.ch


EMBL release 89 is available
----------------------------

The EMBL Nucleotide Sequence Database was frozen to make Release 89 
on 30-NOV-2006. The release contains 83,666,567 sequence entries 
comprising 150,163,403,742 nucleotides, of which 18,535,353 entries 
(81,521,656,204 nucleotides) are WGS (whole genome shotgun) data.
The release 89 files total 69 GB compressed and 376 GB uncompressed.
A breakdown of Release 89 by dataclass and taxonomic division is shown below:
Breakdown by dataclass
Class                                     entries    nucleotides
----------------------------------------------------------------
CON:Constructed                           849,126 62,900,561,886
EST:Expressed Sequence Tag             39,808,988 21,920,348,867
GSS:Genome Sequence Scan               16,073,640 10,211,729,434
HTC:High Throughput CDNA sequencing       450,564    553,627,818
HTG:High Throughput Genome sequencing      97,088 16,352,298,997
PAT:Patents                             3,556,157  2,137,088,250
STD:Standard                            3,399,493 16,630,347,569
STS:Sequence Tagged Site                  890,995    500,504,557
TPA:Third Party Annotation                  5,163    335,802,046
WGS:Whole Genome Shotgun               18,535,353 81,521,656,204
                                        ---------- --------------
Total                                  83,666,567 150,163,403,742
Breakdown by taxonomic division
Division                                  entries    nucleotides
----------------------------------------------------------------
ENV:Environmental Samples               2,162,420  1,545,072,677
FUN:Fungi                               1,488,539  2,230,258,753
HUM:Human                              11,475,120 21,333,688,751
INV:Invertebrates                       9,870,449 15,374,595,645
MAM:Other Mammals                      17,362,895 50,366,774,550
MUS:Mus musculus                        8,167,813 13,853,936,225
PHG:Bacteriophage                           4,081     22,102,277
PLN:Plants                             19,239,706 15,375,178,666
PRO:Prokaryotes                           516,770  3,219,947,843
ROD:Rodents                             3,615,200 15,116,847,721
SYN:Synthetic                             717,339    272,882,442
TGN:Transgenic                                789        458,737
UNC:Unclassified                        1,289,894    590,194,931
VRL:Viruses                               428,087    428,811,568
VRT:Other Vertebrates                   7,327,465 10,432,652,956
                                        ---------- --------------
Total                                  83,666,567 150,163,403,742
Breakdown by both taxonomic division and dataclass can be found in 
divisions.ndx, distributed together with the release

EMBL database statistics are available at
URL: http://www3.ebi.ac.uk/Services/DBStats/

Note: The nucleotide count for CON(structed) entries is included
in the table, but not in the total. The nucleotide count for the
segments of a CON entry is included in the taxonomic divisions.



How to contact us ?
-------------------

Don't forget our official help desk email address:

helpdesk at mail.ch.embnet.org

When sending an email to this address you will automatically receive
a ticket with a number. Your question will be answered by our team
or by an expert in the field from the Swiss Institute of Bioinformatics.

We wish you a Merry Christmas and a Happy New Year.

Laurent Falquet, Swiss EMBnet node manager
and the Swiss EMBnet team members,
Lorenza Bordoli
Vassilios Ioannidis




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