Bioperl: manipulating long strings (genomes) in PERL
Mon, 29 Mar 1999 12:23:33 +0100


I've been told that PERL has no limit on the length of a string it can
handle (memory-wise), but I haven't had it explained why large strings slow
down run time so much.   Can someone explain to me exactly why this is and
more importantly, how best to deal with long strings in PERL - is this a
losing battle, or can I solve it using arrays or some other approach? (In
comparision, True Basic has no problem handling genomes as strings....). I
want to search genome sequences for RE's, whereas previously I had been
searching multi-entry fasta files of all the proteins (short strings) from
sequenced genomes.

So, in short is string size an issue in PERL?

many thanks for any illumination on the subject,

Dawn Field
Oxford Univerisity
Molecular Infectious Diseases Group. IMM
John Radcliffe Hospital
Oxford OX3 9DS


tel: 011-44-1865-222346 or 222347
fax: 011-44-1865-222626

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