UNIX for Dummies Questions & Answers

I am interested in finding a pattern that looks like this

AABBACC

These letters are just for example but they can be any letter in the alphabet as long as they are different from each other, but the letter found in a certain spot should act like in the pattern above.

Thanks!

tested in bash:

Code:

grep -E '(.)\1(.)\2{1}\1(.)\3'

PS:this code cannot filter a sequence of the same leters, such as AAAAAAA.

Wonderful !! but could you please explain us the logic. Its very hard to crack

Thanks, I'm looking for a DNA binding motif, so that some letters of the DNA code repeat in a certain order..

Would you shed some light on how to filter patern AAAAAAAA? thx!

Hi vistastar:

Then one has to do the following:

grep -E '(.)\1(.)\2\1(.)\3' testfile | grep -Ev '.(.)\1.{4}' | grep -Ev '...(.)\1.{2}' | grep -Ev '....(.)\1.' | grep -Ev '...(.).\1.'

the grep -Ev (extended negated option) tests whether second A is not first B '.(.)\1.{4}' and second B is not third A '...(.)\1.{2}' and third A is not first C '....(.)\1.' and second B is not first C '....(.)\1.' -- the other combinations are tested by the first expression. Here is a test of it:

Stefans-Computer:~ stefangr$ echo 'AABBACC' > testfile
Stefans-Computer:~ stefangr$ grep -E '(.)\1(.)\2\1(.)\3' testfile | grep -Ev '.(.)\1.{4}' | grep -Ev '...(.)\1.{2}' | grep -Ev '....(.)\1.' | grep -Ev '...(.).\1.'
AABBACC
Stefans-Computer:~ stefangr$ echo 'AAAACCC' > testfile
Stefans-Computer:~ stefangr$ grep -E '(.)\1(.)\2\1(.)\3' testfile | grep -Ev '.(.)\1.{4}' | grep -Ev '...(.)\1.{2}' | grep -Ev '....(.)\1.' | grep -Ev '...(.).\1.'
Stefans-Computer:~ stefangr$