ITERATIVE APPROACH
iterative tools
PRALINE
Profile Alignment
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Integrate information from database homology searches to generate a homology-extended multiple alignment.
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Can be used through two separate interfaces: one has been designed to cater to more advanced needs of researchers in the field, and the other for standard construction of high confidence alignments.
mechanism of iterative approach
ADVANTAGES
Can overcome the inherent limitation of progressive alignment method
Improves on progressive methods with a more accurate distance measure to assess the relatedness of two sequences
Suitable to align large number of sequences
MSA approaches comparison
Exact
methods
Use dynamic
programming to
generate
optimal alignment
Progressive alignment
Use dynamic
programming to
generate
optimal alignment
Iterative approaches
align multiple
sequence ether
nucleotide or protein sequences
Consistency-based method
Align multiple
nucleotide sequence with an addition of probabilistic model
Structured-based method
Align structural information instead of sequence to get similarities and differences
Alignment
Exact
methods
To
generate
optical alignment
Progressive alignment
Generate guide
tree between multiple sequence alignment
Iterative approaches
Similar to Progressive alignment but undergoes refinement and iteration
Consistency-based method
Model gaps better in an MSA and detect conserved motifs between proteins sequences.
Structured-based method
Find
similarities and differences in form of structure
Exact
methods
Use dynamic
programming which dimension increase when number of alignment increase
Progressive alignment
Undergoes
pairwise alignment which are use to generate guide tree based on similarities
Iterative approaches
Early step similar to progressive alignment but undergoes improvement and refinement by using different programmes
Consistency-based method
Use a database of both local high-scoring alignments and long-range global alignments to create a final alignment
Structured-based method
Aligned the structural information of multiple query and sample to get similarities and differences
Functions
Mechanism
Exact
methods
Not time
feasible
for multiple alignment
(longest in
time taken)
Progressive alignment
Fastest in
comparisons
among
all
five approaches
Iterative approaches
Take longer
time than
progressive alignment due to iterate and
refinement steps
Consistency-based method
Second longest time taken after exact methods due to combining both progressive and iterative approaches with a unique probabilistic model
Structured-based method
Similar to
progressive alignment in
term of time taken
but aligned strucured instead of sequence
Time Taken
Exact
methods
Use dynamic programming
Progressive alignment
ClustalW
Iterative approaches
PRALINE, MUSCLE
Consistency-based method
ProbCons
Structured-based method
T-Coffee : Expresso
Tools
1. Muhammad Iqbal Bin Abu Bakar (192113)
2. Nusyazwan Faiz Bin Nushaimin (194256)
3. Nurul Farhanah Binti Zul (192160)
4. Nur Syakirah Binti Mohammad Mahfud (192064)
5. Nur Syahira Binti Mohd Ariffin (192347)
6. Nur Syazwani Binti Abdul Haziz (192246)
