Regex Question ...

[jay vas]

Hi Im new to java regexes. I need to build a regex that detects
all words in a paragraph that look like a string of amino acids.

So for example :

Ala-Cys-Ala, A-C-A, and ACA all represent possible amino acid sequences of alanine, cystein and alanine. Is there a way to build a regex in java that represents this ? Currently Im doing it with nested for loops. Ive tried
[A|Ala|V|Val|L|Lys|M|Met|W|Trp|P|S|T|Thr|C|Y|Tyr|N|Asn|-|Q|D|E|K|R|H|X]++ but it returns false positive matches... for example GAVs is returned as group(0) using the java matcher, even though the 's' character is not in the expression..?

Ala A
Arg R
Asn N
Asp D
Cys C
His H
Ile I
Leu L
Lys K
Met M
Phe F
Pro P
Ser S
Thr T
Trp W
Tyr Y
Val V

[Jeanne Boyarsky]

Jay,
group(0) returns the whole matching string, not just the matching portion. Try putting your reg exp in parens and using group(1).

[jay vas]

Well ive gotten closer, but for some reason
EEEs matches ... any ideas?

 
 
import java.util.regex.Matcher;
import java.util.regex.Pattern;
 
// Biojava imports 
 
class BioinformaticsUtilities 
{
static String[] tests =new String[]{"GAVXC","CYXC","EE","EXEXXEs"};
static String P ="([G|A|V|L|[Lys]{3}|M|F|W|P|S|T|[Thr]{3}|C|Y|[Trp]{3}|N|-|Q|D|E|K|R|H|X]){3,9}?";

//static String[] tests =new String[]{"GGLysA"};
//static String P ="(G|A|V|[Lys]{3}){1,3}?";
 

public static void main(String[] args) 
{
for(String test : tests)
if(Pattern.matches(P, test))
System.out.println("Match ! " + test);
else
System.out.println("NO    Match !" + test);
}
}

[Henry Wong]

static String P ="([G|A|V|L|[Lys]{3}|M|F|W|P|S|T|[Thr]{3}|C|Y|[Trp]{3}|N|-|Q|D|E|K|R|H|X]){3,9}?";

This pattern makes no sense... what is it that you are trying to do?

Henry

[jay vas]

"([G|A|V|L|[Lys]{3}|M|F|W|P|S|T|[Thr]{3}|C|Y|[Trp]{3}|N|-|Q|D|E|K|R|H|X]){3,9}?";


The pattern means

Match a strings which is
1) of length 3 through 9
where
2) all subStrings in the string are a combination of
G,A,V,L,Lys, M,F,W,P,S,T,Thr, C,Y,Trp, N, -, Q, D, E, K, R, H, or X.


so

G-A-V-L-X-L matches
Lys-L-V-G-A-Trp-X-Trp matches
but


Lys-O-Lys-X wouldnt match (since O is not a valid amino acid).
Also
A-L-s-L-s-X wouldnt match either (s isnt an amino acid, although S is).

[Henry Wong]

"([G|A|V|L|[Lys]{3}|M|F|W|P|S|T|[Thr]{3}|C|Y|[Trp]{3}|N|-|Q|D|E|K|R|H|X]){3,9}?";

The pattern means

Match a strings which is
1) of length 3 through 9
where
2) all subStrings in the string are a combination of
G,A,V,L,Lys, M,F,W,P,S,T,Thr, C,Y,Trp, N, -, Q, D, E, K, R, H, or X.

Sorry, but the pattern that you have doesn't do what you described. In fact, I am not even sure if some of the stuff in the pattern is even valid.

Assuming that the "-" is an optional separator, and not part of the sequence, this is probably closer to what you want...

static String P = "((([GAVLMFWPSTCYNQDEKRHX])|(Lys)|(Thr)|(Trp))-?){3,9}";

Henry

[jay vas]

Thanks !!! I'lll try it and tell you the result. BTW, what does the ? after the - mean ?

[Rob Spoor]

It means the - is optional.