Motifs in Bioinformatics
Dr Sajith Ahamed
Assistant Professor
Department of Microbiology
HKRH College
Subject Name –
Bioinformatics
Subject Code –
17UMBE51
Semester : V
Programme : B.Sc.Microbiology
Moti
f
s
•
Defined
as a
nucleotide
or amino acid
sequence
pattern
that
is
widespread
and is
associated
with a
biological
function
.
–
A
sequence
motif = A
structural
Motif.
–
A
sequence
motif
residing
in the
coding region
may
encode
a
structural
motif
.
–
Non-coding nucleotide motifs
may
have
regulatory
role. May
have
recognition sites
for
DNA
binding proteins.
Motifs,
profiles
and
patterns
•
Conserved region
of a DNA or
protein
–
Motif
•
Qualitative expression
of
a motif –
Pattern
–
Regular
Expression
–
C[TA]TTG{X}•
Quantitative expression
of
a motif –
Profile
–
Position
Specific Scoring Matrices
(PSSMs)
–
Weight
matrices
Motifs/Patterns
N{P}[ST]{P}[FILV]Qxxx[RK]Gxxx[RK]xx[FILVWY]
[] ->
or
(Probability
information
is
lost)
{} ->
Not
()
->
repeated
^ ->
Beginning
De
novo
prediction
of
Motifs
•
MEME;
EXTREME; AlignAce, Amadeus, CisModule, FIRE, Gibbs
Motif
Sampler,
PhyloGibbs,
SeSiMCMC
,
ChIPMunk
and
Weeder.
SCOPE
,
MotifVoter,
and
Mprofiler
MEME
(Multiple
Expectation
Maximization
for
Motif
Elicitation)
MacIsaac
KD, Fraenkel
E
(2006) Practical Strategies
for
Discovering
Regulatory
DNA
Sequence Motifs.
PLoS
Comput Biol
2(4): e36.
doi:10.1371/journal.pcbi.0020036
http://journals.plos.org/ploscompbiol/article?id=info:doi/10.1371/journal.pcbi.0020036
MRLSFVPLLQLSRLVVSTQHSTKMSTVYRTCKMNEIALSLLAPTQPLDADQGVMSPMASSDQ
TTSIGDFRFLRTHHDKEERGLLVTSLTKGLAETSFPYR
YTSMCATICSITHSRADAAPAKQAH
P
r
osi
t
e
ATGCGTCTCTCCTTCGTTCCACTACTGCAGCTCTCTCGTCTGGTCGTTAGCACACAACATAGTACGAAAATGA
GCACAGTATACCGTACCTGCAAAATGAATGAAATAGCTCTCTCGTTGCTGGCGCCAACGCAGCCATTGGACG
CTGACCAGGGTGTTATGTCACCGATGGCCTCATCAGACCAGACAACCTCAATTGG TGACTTTCGGTTCCTGA
GAACCCACCACGATAAAGAAGAGCGGGGCTTGCTGGTTACCAGCCTCACAAAAGGTTTGGCTGAAACATCAT
TTCCGTATCGATACACTTCGATGTGCGCAACTATTTGTTCAATTACGCATTCTCGGGCAGATGCTGCGCCTGC GAAGCAGGCGCACTA
Scan
this sequence
and
get
me the
motif
OR Build
a
PSSM
A
T
GCGTCTCTC A
T
GCCTC
T
G
T
C
A
T
GCGTCTCTC A
T
GCGTCTCTC
A
T
GCGTCTA
T
C
Bioinformatics studies the patterns of sequences called motifs, which play significant roles in biological functions. Conserving information from DNA or proteins, motifs can be predicted de novo using various tools and strategies. Exploring these motifs aids in understanding regulatory elements and functional regions within biological sequences.
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Presentation Transcript
Subject Name Subject Code Semester : V Programme : Subject Name Bioinformatics Subject Code 17UMBE51 Semester : V Programme : B.Sc.Microbiology Bioinformatics 17UMBE51 B.Sc.Microbiology Dr Sajith Ahamed Assistant Professor Department of Microbiology HKRH College
Motifs Defined as a nucleotide or amino acid sequence pattern that is widespread and is associated with a biological function. A sequence motif = A structural Motif. A sequence motif residing in the coding region may encode a structural motif. Non-coding nucleotide motifs may have regulatory role. May have recognition sites for DNA binding proteins.
Motifs, profiles and patterns C[TA]TTG{X} C T T T G X Conserved region of a DNA or protein Motif Qualitative expression of a motif Pattern Regular Expression C[TA]TTG{X} C A T T G X [TA] C T T G any Quantitative expression of a motif Profile Position Specific Scoring Matrices (PSSMs) Weightmatrices
Motifs/Patterns N{P}[ST]{P} [FILV]Qxxx[RK]Gxxx[RK]xx[FILVWY] [] -> or (Probability information is lost) {} -> Not () -> repeated ^ -> Beginning
De novo prediction of Motifs MEME; EXTREME; AlignAce, Amadeus, CisModule, FIRE, Gibbs Motif Sampler, PhyloGibbs, SeSiMCMC, ChIPMunk and Weeder.SCOPE, MotifVoter, and Mprofiler MEME (Multiple Expectation Maximization for Motif Elicitation)
MacIsaac KD, Fraenkel E (2006) Practical Strategies for Discovering Regulatory DNA Sequence Motifs. PLoS Comput Biol 2(4): e36. doi:10.1371/journal.pcbi.0020036 http://journals.plos.org/ploscompbiol/article?id=info:doi/10.1371/journal.pcbi.0020036
MRLSFVPLLQLSRLVVSTQHSTKMSTVYRTCKMNEIALSLLAPTQPLDADQGVMSPMASSDQMRLSFVPLLQLSRLVVSTQHSTKMSTVYRTCKMNEIALSLLAPTQPLDADQGVMSPMASSDQ TTSIGDFRFLRTHHDKEERGLLVTSLTKGLAETSFPYR YTSMCATICSITHSRADAAPAKQAH
Scan this sequence and get me the motif ATGCGTCTCTCCTTCGTTCCACTACTGCAGCTCTCTCGTCTGGTCGTTAGCACACAACATAGTACGAAAATGA GCACAGTATACCGTACCTGCAAAATGAATGAAATAGCTCTCTCGTTGCTGGCGCCAACGCAGCCATTGGACG CTGACCAGGGTGTTATGTCACCGATGGCCTCATCAGACCAGACAACCTCAATTGG GAACCCACCACGATAAAGAAGAGCGGGGCTTGCTGGTTACCAGCCTCACAAAAGGTTTGGCTGAAACATCAT TTCCGTATCGATACACTTCGATGTGCGCAACTATTTGTTCAATTACGCATTCTCGGGCAGATGCTGCGCCTGC GAAGCAGGCGCACTA TGACTTTCGGTTCCTGA OR Build aPSSM ATGCGTCTCTC ATGCGTCTCTC ATGCGTCTATC ATGCCTCTGTC ATGCGTCTCTC
