Without giving you the explicit answers, here's some things to think about that you may or may not already know:

• Don't forget to reverse-complement the DNA sequence and search for reading frames. Look at the reverse and tr functions for some help with that.
• An ORF is only valid if the start and stop codons are "in-frame," which means that the length of the ORF is divisible by three with no remainder.
• Most definitions of a valid ORF will not allow any in-frame stop codons. So, for example, the sequence start-start-stop is a valid ORF, but the sequence with start-stop-stop is not. There's exceptions to this (there are always exceptions in biology), but I doubt they are relevant to what you're doing.

Good luck. :)

---

---

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! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

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:
	&		&
	<		&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.