SLiMMaker (SLiM stands for Short, Linear Motif) is regular expression generator that takes as input sequences and creates from them a regular expression that matches all the inputs.

URL: http://bioware.soton.ac.uk/slimmaker.html

Here is an example:

Input:

QGTLESFFKR
QKRINEFFPR
QGRLDDFFKV
QSSLLSFFSK
QPTISRFFKK
QGRLDGFFQV
QRSIMSFFHP
QTTITSHFAK
QKTLYSFFSP
QKSIMSFFGK
QATLARFFTS
QQTLSSFFMG
QTTIEDFFGT
QVSITGFFQR
QTSMTDFYHS
QLRIDSFFRL
QSTLYSFFPK
QWKLLRDFDI

Output:

Q.[RST][IL].[DRS]FF