index has already been mentioned, but I wanted to comment on this:

Only one hit is possible for each 'probe' string

It is possible that the probes have already been screened for uniqueness, but based on a frequency of 0.25 for each base (on average and subject to inter-species variation, of course) a 10-mer would occur by chance once every 1,048,576 bases (4**10). Your chromosomes are 30 million bases long, so in the absence of other information I'd expect each probe to match quite a few times on each chromosome.

That said, note that the third parameter of index sets the start position for searching the string. To find all matches you'll have to use index iteratively, m//g, or (the approach I prefer, BrowserUk++) create an index of the chromosomes before searching for your 1 million probes.

In reply to Re: pattern match, speed problem by bobf
in thread pattern match, speed problem by spring

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.