comment on

I suspect, based on previous similar questions of this type, that what the op has is:

A bunch of long sequences; possibly 1000s or 100,000s bytes/codons/other long.
A bunch of shorter sequences perhaps 10 chars, perhaps 9 or 10 chars, long.

And the process he's trying to code is:

For each of the long sequences...
For each of the short sequences...
Scan the longer sequence looking for sites where the shorter sequence 'matches' and record those positions.

The complication is that the matching is 'fuzzy' within his set of constraints:

such that a 9 character subsection of the larger sequence may be considered a match to a 10-character short sequence, if (for example) the removal of any (exactly one) character from the 10 character sequence allows it to match the 9 character subsection of the longer sequence.
Or, a 10-character short sequence may be considered a match for a 10-character subsection of the longer sequence if they differ in exactly (only) one position.

But, that's just supposition until he answers somebody's questions!

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority". I'm with torvalds on this

In the absence of evidence, opinion is indistinguishable from prejudice. Agile (and TDD) debunked

In reply to Re^6: Filtering matches of near-perfect-matched DNA sequence pairs by BrowserUk
in thread Filtering matches of near-perfect-matched DNA sequence pairs by onlyIDleft

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:
	&		`&`
	<		`<`
	>		`>`
	[		`[`
	]		`]`

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.