[BiO BB] pattern & Motif (A.S.Kiran)

Ayyagari Kiran kiran_ayyagari at yahoo.com
Tue Dec 4 05:33:46 EST 2001

Hi Nikhil,

Hope this summary would clear your doubt.

A pattern represents any type of sub-sequence that
fits the regular expression defined( For instance,
C-X(2,4)-[DE] is a sequence pattern matching any
sequence containing a sub-string starting with C,
followed by between two and four arbitrary symbols,
followed by either a D or an E. This pattern is an
example of a deterministic pattern.likewise there are
probabilistic patterns(Profile HMMs)

Sequence and structure patterns can be used for
characterising protein families which are defined to
be sets of functionally or structurally related
Motifs are short patterns that repeat quite often
within a given set of protein sequences,(with some
variations) and usually serve some important
functional role from a biochemical viewpoint
representing information conserved during the process
of evolution..
A motif may typically contain information regarding
the tertiary structures of the proteins and other
biological information, whereas, a pattern occurs more
of a statistical presence than a biological one. On a
general basis a pattern can be defined as a motif, if
it is conserved strongly within a given set of
It is also important to note that all motifs are
patterns but, not all patterns are motifs. 


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