a question regarding bioinfomatics - (Oct/23/2006 )

Hi,

I try to identify some proteins having the cis-regulatory elements of one transcription factor. I knew that the factor can recognize 5'-GGAAA-3' sequence. Is there some software which can help me to find out those proteins?

-yiwuya-

If you known that GGAAA motif is conserved along all your proteins, you could write a perl program for do this task.

If not you may be could use HMM to identify the motif.

-djv0022-

QUOTE (djv0022 @ Oct 23 2006, 06:24 PM)

If you known that GGAAA motif is conserved along all your proteins, you could write a perl program for do this task.

If not you may be could use HMM to identify the motif.

Sorry, what is HMM?

-yiwuya-

QUOTE (yiwuya @ Oct 24 2006, 09:38 AM)

QUOTE (djv0022 @ Oct 23 2006, 06:24 PM)

If you known that GGAAA motif is conserved along all your proteins, you could write a perl program for do this task.

If not you may be could use HMM to identify the motif.

Sorry, what is HMM?

hi yiwuya,

are u trying to say that u want to identify proteins that can recognize the "GGAAA motif" ....

while this sounds like a big task for me.......however, what u can do is see what proteins that have been known already that interact with that motif....like any information on the GGAAA interacting protein domain...or sequence conservation among a set of proteins that interact with that motif....

if ur able to observe some sequence conservation...then it might be good to think further of trapping proteins that would interact with that motif.....i guess

-string-

HMM = hidden markov model see wikipedia

-perlmunky-