Indexing EMBL 51
Andrew T. Lloyd
atlloyd at tcd.ie
Fri Jul 4 03:20:31 EST 1997
Hi SRS giants,
It would not be strictly true for me to claim that the workings
of SRS are totally opaque to me. It would be a close approx tho.
I have three questions which probably have obvious answers.
Indexing EMBL 51 took 32 HOURS. During this time, my
users get disturbingly wrong info, presmably because the
partly built indexes point to the old parts of the flatfiles ?
Q1. Is it possible to dump the new indexes to a temporary
directory, maintaining full functionality with the old DBs
and when the indexing is finished switch it all over in say
32 seconds ?
At vast (and I mean VAST) expense, I bought another 256MB
memory last year.
Q2. Is it possible to rejig the indexing protocol
so that it uses more than, say, 90MB and thus goes through
And finally on the real noddy level:
Q3. Once I've clagged all my SW:reca_* into one list, how do
I extract them as, say, a concatenated fasta file which I can
zing through clustalW.
Thanks for your help,
Andrew T. Lloyd Irish National Centre for BioInformatics INCBI
atlloyd at acer.gen.tcd.ie http://acer.gen.tcd.ie
Tel: (+353)-1-608-1969 EMBnet Ireland Fax: (+353)-679-8558
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