EMBNet News bulletin of 08-Jun-1998

Laurent Falquet Laurent.Falquet at isrec.unil.ch
Mon Jun 8 18:46:47 CEST 1998


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* EMBNet News bulletin of 08-Jun-1998 *
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Implementation of NCBI-BLAST version 2.0
-----------------------------------------

Thanks to Christian Iseli, our implementation of NCBI-BLAST version 2.0
is running on a new 4-processor 200Mhz Pentium-Pro machine. You should
notice
a sizable improvement in performance over the current BLAST server.

The link to the web page to access BLAST2.0 can be found at:
http://www.ch.embnet.org/database_search.html

Two forms are available, a "basic" form for simple queries and an
"advanced" form for more complex queries.
The "tblastn" and "tblastx" programs return the results by e-mail, thus you
must provide an e-mail address in the query form.

For people using BLAST from the command line, please use the "blastall"
command:

"blastall.remote [client side options] -p <program> [-d] <database> [-i]
<query file> [blastall options]"

We can provide BLAST clients compatible with our server for all major
Unix platforms.


New databases available for search with BLAST2.0
--------------------------------------------------

Thanks to Dr. Philipp Bucher, you can search the Unigene human and mouse
databases. These are collections of clusters of sequences, each cluster
contains the list of all known ESTs, STSs and Human Transcript that match
a single gene. However, the corresponding assembled sequence is not
provided. Searches on Unigene allow you to rapidly identify all ESTs and
GenBank cDNA entries that derive from the same gene as your query.

The Radiation Hybrid database is a collection of EMBL entries corresponding
to sequences that have been mapped using the radiation hybrid methodology.
A search on this database will return chromosomal localizations, and the
results
of RH mapping experiments. The latter can be used to generate a precise
genetic
map for the region surrounding marker under consideration.

Have fun with those new features!

Best regards,

Laurent Falquet. (Please do not hesitate to contact me in case of problems
with the pages or the results)

-----------------------------------------
Dr. Laurent Falquet
Bioinformatics Group
Swiss Institute for Experimental Cancer Research (ISREC)
Ch. des Boveresses 155
CH-1066 Epalinges
Switzerland

Tel: +41 (21) 692 5820
FAX: +41 (21) 653 4474
Email: Laurent.Falquet at isrec.unil.ch




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