[Seqinr-forum] frozen version of EMBL / mirror of ACNUC?

[Coghlan, Avril]

Dear Jean,

Thank you for your suggestion of using the frozen version of EMBL for
the practical, that is a good idea.

I am wondering whether it is at all possible for me to create a mirror
or local copy of the frozen version of EMBL (or any other ACNUC database
that SeqinR can access), for the students to use just in case the ACNUC
databases are down on the day of my practicals?

Regards,
Avril

-----Original Message-----
From: Jean lobry [mailto:lobry at biomserv.univ-lyon1.fr] 
Sent: 15 November 2009 10:41
To: seqinr-forum at r-forge.wu-wien.ac.at
Cc: Coghlan, Avril
Subject: Re: [Seqinr-forum] searching for sequences from Aspergillus
nidulans in 'genbank'
For a practical for students I would suggest to use frozen databases.
They are accessible with the special value "TP" for the "tagbank"
argument on opening (TP means "Travaux Pratiques" which is french
for practicals).

######
>  library(seqinr)
>  choosebank(tagbank = "TP")
[1] "emblTP"      "swissprotTP" "hoverprotTP" "hovernuclTP" "trypano"
>  choosebank("emblTP")
>  banknameSocket$details
[1] "             ****     ACNUC Data Base Content      **** 
"
[2] "              EMBL Library Release 78 WITHOUT ESTs  (March 2004)"
[3] "27,571,397,913 bases; 12,533,594 sequences; 1,604,500 subseqs; 
339,186 refers."
[4] "Software by M. Gouy & M. Jacobzone, Laboratoire de biometrie, 
Universite Lyon I "
>  query("anidulans","SP=aspergillus nidulans")
>  anidulans$nelem
[1] 218
######

There are only 218 sequences for Aspergillus nidulans in this frozen
version of EMBL, but the advantage is that the results are stable over
time. Your practical will be ready unchanged for next year.

Best,
-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/