EMBnet News bulletin of 24 Sep 2004

Laurent Falquet Laurent.Falquet at isrec.unil.ch
Fri Sep 24 14:23:28 CEST 2004

* EMBnet News bulletin of 24-Sep-2004 *

Dear Users,

Announcing the MyHits web server

The MyHits web server (http://myhits.isb-sib.ch) is a new integrated
service dedicated to the annotation of protein sequences and to the
analysis of their domains and signatures. Guest users can use the
system anonymously, with full access to (i) standard bioinformatics
programs (e.g. PSI-BLAST, ClustalW, T-Coffee, Jalview); (ii) a large
number of protein sequence databases, including standard (Swiss-Prot,
TrEMBL) and locally developed databases (splice variants); (iii)
databases of protein motifs (Prosite, Interpro); (iv) a precomputed
list of matches ('hits') between the sequence and motif databases.
All databases are updated on a weekly basis and the hit list is kept
up to date incrementally. The MyHits server also includes a new
collection of tools to generate graphical representations of pairwise
and multiple sequence alignments including their annotated features.
Free registration enables users to upload their own sequences and
motifs to private databases. These are then made available through
the same web interface and the same set of analytical tools.
Registered users can manage their own sequences and annotations using
only web tools and freeze their data in their private database for
publication purposes.

EMBL 80 is available

The EMBL Nucleotide Sequence Database was frozen to make Release 80 on
24-AUG-2004. The release contains 42,312,264 sequence entries
comprising 70,222,432,184 nucleotides,of which 4,429,392 entries
(28,144,536,717 nucleotides) are WGS (whole genome shotgun) data.

A breakdown of Release 80 by division is shown below:

Standard entries + CON entries

Division               Entries     Nucleotides
----------------- ------------ ---------------
Constructed            237,125  11,247,419,471
ESTs                23,226,531  12,155,781,188
Fungi                  103,689     213,846,265
GSSs                 9,568,613   5,842,988,064
HTC                    319,378     394,376,377
HTG                     68,249  11,651,940,375
Human                  286,208   4,105,680,727
Invertebrates          164,185     658,854,200
Other Mammals           66,895     309,757,479
Mus musculus            93,487   2,062,521,054
Organelles             290,615     247,758,715
Patents              2,163,417   1,229,006,974
Bacteriophage            2,552      12,508,260
Plants                 264,451   1,034,367,364
Prokaryotes            264,829     896,017,378
Rodents                 29,568     105,425,332
STSs                   375,750     166,015,652
Synthetic               12,488      20,842,721
Unclassified             2,507       2,611,052
Viruses                243,393     224,005,681
Other Vertebrates       98,942     743,590,609
                   ------------ ---------------
Total               37,882,872  42,077,895,467

WGS entries
Division               Entries     Nucleotides
----------------- ------------ ---------------
Fungi                   21,346     395,046,388
Human                  601,855   8,075,925,526
Invertebrates          413,451   2,005,707,197
Other Mammals        1,947,020   9,299,027,304
Mus musculus           224,733   2,570,248,549
Plants                 103,044     363,323,500
Prokaryotes             16,100     307,764,658
Rodents                137,910   2,571,104,688
Unclassified           813,827     826,809,393
Viruses                     88         646,990
Other Vertebrates      150,018   1,728,932,524
                   ------------ ---------------
Total                4,429,392  28,144,536,717

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.

Courses in 2005

We plan to organise several courses in 2005. We will announce them
towards the end of 2004. Here is a preliminary list (susceptible to changes):

Introduction to Bioinformatics
Advanced 3D structure of Proteins
Introduction to the RNA world (iRNA, siRNA, miRNA, tRNA, rRNA, snRNA, 
telRNA, etc.)
Perl language and UNIX tools for Biologists (How to automate your work)

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.

Best regards,

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