Understanding Amino Acid Patterns.

Question

[Caitlin]

HI all.

I was wondering if someone could please explain the meaning of an amino acid pattern, e.g.,

P.{12,26}[AILV].NP[LN]

If so, please do not post any code. All I need to do is understand the meaning of the above syntax.

Thanks,

~Caitlin

Answer 1

[komal.rathi]

• P -> Proline
• . -> any amino acid
• {12,26} -> between 12 to 26 times. So .{12,26} together means any sequence of amino acid of length between 12 and 26
• [AILV] -> any amino acid from Alanine, Isoleucine, Leucine, Valine but just one time
• . -> any amino acid but just once
• N -> Asn
• P -> Pro
• [LN] -> any amino acid from Leucine or Asparagine but just once

Answer 2

[JacobS]

This is just semi-universal regular expression (regex) syntax, but with single letter abbreviations for the amino acids. Using a cheat sheet like the following might be very helpful: http://ult-tex.net/info/perl/. A general intro to regular expressions (in this case perl) is found here: http://www.cs.tut.fi/~jkorpela/perl/regexp.html. Hope it helps!