BLOG | Mysite

ITERATIVE APPROACH

iterative tools

MUSCLE

Multiple Sequence Comparison by Log Expectation

This program can achieve both better average accuracy and better speed.
MUSCLE uses FASTA format for both input and output.
It also offers CLUSTALW, MSF, HTML, Phylip sequential and Phylip interleaved formats for output.

Find out More

PRALINE

Profile Alignment

Integrate information from database homology searches to generate a homology-extended multiple alignment.
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.

Find out More

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

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

WhatsApp Image 2019-05-22 at 3.18.46 AM.

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)

mohammad iqbal abu bakar

May 23, 20191 min read

ITERATIVE APPROACHES

Learn more about MSA.

ITERATIVE APPROACH

iterative tools

MUSCLE

Multiple Sequence Comparison by Log Expectation

PRALINE

Profile Alignment

ADVANTAGES

MSA approaches comparison

Exact

methods

Progressive alignment

Iterative approaches

Consistency-based method

Structured-based method

Alignment

Exact

methods

Progressive alignment

Iterative approaches

Consistency-based method

Structured-based method

Exact

methods

Progressive alignment

Iterative approaches

Consistency-based method

Structured-based method

Functions

Mechanism

Exact

methods

Progressive alignment

Iterative approaches

Consistency-based method

Structured-based method

Time Taken

Exact

methods

Progressive alignment

Iterative approaches

Consistency-based method

Structured-based method

Tools

ITERATIVE APPROACHES

join our mailing list