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Mutiple Motifs

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Each fingerprint has been defined and iteratively refined using database SWISS ... Fingerprints can encode protein folds and functionalities more flexibly and ... – PowerPoint PPT presentation

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Title: Mutiple Motifs


1
Mutiple Motifs
  • Charles Yan
  • Spring 2006

2
Mutiple Motifs
3
From Single Motif to Multiple Motifs
  • One single motif is not sufficent to discriminate
    a protein family. Multiple motifs have stronger
    discriminating power.

4
Multiple Motifs
  • Protein function prediction using multiple motifs
  • Each protein family is characterized by a set of
    motifs (in stead of a single one).
  • If a protein contain a set of motifs, it probably
    belong to the family that the set of motifs
    correspond to.

5
PRINTS
  • PRINTS (http//umber.sbs.man.ac.uk/dbbrowser/PRINT
    S/ ) is a database of protein fingerprints.
  • A fingerprint is a group of conserved motifs used
    to characterize a protein family
  • ftp.bioinf.man.ac.uk/pub/prints
  • PRINTS is now maintained at the University of
    Manchester
  • PRINTS VERSION 38.0 (16 June, 2005)
  • 1900 FINGERPRINTS, encoding 11,435 single motifs

6
PRINTS
  • Each fingerprint has been defined and iteratively
    refined using database SWISS-PROT/TrEMBL
    composite.
  • Two types of fingerprint are represented in the
    database, i.e. they are either simple or
    composite, depending on their complexity simple
    fingerprints are essentially single-motifs while
    composite fingerprints encode multiple motifs.
    The bulk of the database entries are of the
    latter type because discrimination power is
    greater for multi-component searches.
  • Usually the motifs do not overlap, but are
    separated along a sequence, though they may be
    contiguous in 3D-space.
  • Fingerprints can encode protein folds and
    functionalities more flexibly and powerfully than
    can single motifs, full diagnostic potency
    deriving from the mutual context provided by
    motif neighbors.

7
PRINTS
  • A motif is a conserved element corresponding to a
    region whose function or structure is known. It
    is likely to be predictive of any subsequent
    occurrence of such a structural/functional region
    in any other protein sequence.
  • A motif is represented as a conserved alignment
    of multiple sequence.
  • A fingerprint is a set of motifs used to predict
    the occurrence of similar motifs, either in an
    individual sequence.

8
PRINTS
9
PRINTS
  • The starting point is a multiple sequence
    alignment of a small number of sequences
  • Once a motif, or set of motifs, has been
    identified, the conserved regions are excised in
    the form of local alignments
  • The motif/s are used to scan against the database
  • Only those sequences that match with all motifs
    are regarded as true matches
  • The additional sequence data from the new true
    set is then used to generate another set of
    aligned motifs, and the database is searched
    again
  • Until converge

10
PRINTS
11
PRINTS
12
PRINTS
  • a) General field

13
PRINTS
  • b) Summary field
  • A good fingerprint should exhibit a clear
    discrimination cut-off, i.e. shows all true
    positives matching with all n motifs, perhaps
    some noise, and few or no matches at intermediate
    positions of the summary table.

14
PRINTS
  • Motif name
  • Iteration number
  • PCODE the protein identification codes of the
    initial sequences
  • ST the location of the motifs within those
    sequences,
  • INT and the interval between adjacent motifs.
    for the first motif, this is simply the distance
    from the beginning of the sequence to the start
    of the motif.

15
PRINTS
16
PRINTS
  • FPScan
  • Submitting a PROTEIN sequence find the closest
    matching PRINTS fingerprint/s.

17
PRINTS
18
PRINTS
19
PRINTS
20
PRINTS
21
PRINTS
  • GRAPHScan
  • A graphical view of the result of a scan of a
    fingerprint against a sequence. Matching motifs
    are highlighted if they score above the threshold
    identity

22
PRINTS
23
PRINTS
24
PRINTS
  • MULScan
  • This facility allows multiple sequences to be
    scanned against the database, Results are
    returned via email.

25
Related Projects
  • InterPro - Integrated Resources of Proteins
    Domains and Functional Sites
  • BLOCKS - BLOCKS db
  • Pfam - Protein families db (HMM derived) Mirror
    at St. Louis (USA)
  • PRINTS - Protein Motif fingerprint db
  • ProDom - Protein domain db (Automatically
    generated)
  • PROTOMAP - An automatic hierarchical
    classification of Swiss-Prot proteins
  • SBASE - SBASE domain db
  • SMART - Simple Modular Architecture Research Tool
  • TIGRFAMs - TIGR protein families db
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