BIOINFORMATICS FOR PHARMACY
PBI20101P
Pairwise Sequence Alignment and Multiple
Sequence Alignment using CLUSTALW & BLAST
, Experiment 3: Pairwise Sequence Alignment and Multiple Sequence Alignment
using CLUSTALW & BLAST
Aim:
To perform pairwise and multiple sequence alignment using both CLUSTALW &
BLAST tools.
Introduction:
A sequence alignment is a method of arranging DNA, RNA, or protein sequences to
find patterns of similarity that may be the result of functional, structural, or evolutionary
links between them. Nucleotide or amino acid residue sequences that are aligned are
often represented as rows in a matrix. To align identical or similar characters in
successive columns, gaps are introduced between the residues. By hand, we can align
very short or highly comparable sequences. Most fascinating tasks, on the other hand,
necessitate the alignment of long, highly variable, or exceedingly numerous sequences,
which cannot be accomplished purely through human effort. There are two types of
computational techniques to sequence alignment: global alignments and local
alignments. The best-matching piecewise (local or global) alignments of two query
sequences are found using pairwise sequence alignment algorithms. Pairwise
alignments may only be utilized between two sequences at a time, but they are quick to
compute and are frequently used for approaches that don't require extreme precision,
such as scanning a database for sequences that are very similar to a query. Dot-matrix
methods, dynamic programming, and word approaches are the three main approaches
for obtaining pairwise alignments. Even though each technique has its own set of
advantages and disadvantages, all three pairwise approaches struggle with extremely
repeated sequences with little information richness, especially when the number of
repetitions in the two sequences to be aligned differs. Multiple sequence alignment is a
variation of pairwise alignment that allows more than two sequences to be aligned at the
same time. All of the sequences in a query set are aligned using multiple alignment
algorithms. Multiple alignments are frequently used to find conserved sequence areas
across a group of sequences that are thought to be related evolutionarily.
One of the key distinctions between local and global alignment is their definition. Local
alignment finds local regions with the highest amount of similarity between the two
sequences, whereas global alignment attempts to align the entire sequence. EMBOSS
Needle and Needleman-Wunsch Global Align Nucleotide Sequences are two alternative
techniques for global alignment. BLAST, EMBOSS Water, and LALIGN, on the other
hand, are applications for local alignment. Global alignment serves the purpose of
containing all letters from both the query and target sequences. It aligns a substring of
the query sequence to a substring of the target sequence for local alignment. Global
, alignments are commonly used to compare homologous genes, such as two genes that
perform the same function or two proteins that perform the same function. Local
alignment, on the other hand, is used to detect conserved patterns in DNA sequences,
as well as conserved domains or motifs in two proteins.
ClustalW is a tool for quickly aligning numerous nucleotide or protein sequences. It
employs progressive alignment methods, in which the most similar sequences are
aligned first, followed by the least similar sequences, until a global alignment is
achieved. T-Coffee and Dialign are consistency-based methods, whereas ClustalW is a
matrix-based approach. ClustalW provides a reasonably efficient algorithm that
outperforms other software. To calculate a global alignment, this program requires three
or more sequences. Between sequences, BLAST discovers regions of local similarity.
The program compares nucleotide or protein sequences to databases of sequences
and estimates their statistical significance. BLAST may be used to infer functional and
evolutionary links between sequences, as well as identify gene family members.
Procedure:
A. CLUSTALW
1. Open the web browser and type https://www.ebi.ac.uk/Tools/msa/clustalw2/.
2. Upload the sequences from the Notepad or paste the sequences in FASTA format.
3. Upload two sequences for pairwise alignment or more than two sequences for
multiple sequences alignment. After uploading, choose the “Execute Multiple Alignment”
option in the alignment icon.
4. Sequence alignment results will be appeared within few seconds after execution.
5. Report the result.
B. BLAST
1. Open the web browser and type http://blast.ncbi.nlm.nih.gov/Blast.cgi
2. Click either nucleotide blast or protein blast icon according to the requirement.
3. Select “Align two or more sequences” check box for opting multiple sequence
alignment or deselect for pairwise alignment.
4. Upload or paste a query sequence (in FASTA format) in the query box and execute
BLAST for pairwise alignment. This will be identifying most similar sequences from the
databank.
PBI20101P
Pairwise Sequence Alignment and Multiple
Sequence Alignment using CLUSTALW & BLAST
, Experiment 3: Pairwise Sequence Alignment and Multiple Sequence Alignment
using CLUSTALW & BLAST
Aim:
To perform pairwise and multiple sequence alignment using both CLUSTALW &
BLAST tools.
Introduction:
A sequence alignment is a method of arranging DNA, RNA, or protein sequences to
find patterns of similarity that may be the result of functional, structural, or evolutionary
links between them. Nucleotide or amino acid residue sequences that are aligned are
often represented as rows in a matrix. To align identical or similar characters in
successive columns, gaps are introduced between the residues. By hand, we can align
very short or highly comparable sequences. Most fascinating tasks, on the other hand,
necessitate the alignment of long, highly variable, or exceedingly numerous sequences,
which cannot be accomplished purely through human effort. There are two types of
computational techniques to sequence alignment: global alignments and local
alignments. The best-matching piecewise (local or global) alignments of two query
sequences are found using pairwise sequence alignment algorithms. Pairwise
alignments may only be utilized between two sequences at a time, but they are quick to
compute and are frequently used for approaches that don't require extreme precision,
such as scanning a database for sequences that are very similar to a query. Dot-matrix
methods, dynamic programming, and word approaches are the three main approaches
for obtaining pairwise alignments. Even though each technique has its own set of
advantages and disadvantages, all three pairwise approaches struggle with extremely
repeated sequences with little information richness, especially when the number of
repetitions in the two sequences to be aligned differs. Multiple sequence alignment is a
variation of pairwise alignment that allows more than two sequences to be aligned at the
same time. All of the sequences in a query set are aligned using multiple alignment
algorithms. Multiple alignments are frequently used to find conserved sequence areas
across a group of sequences that are thought to be related evolutionarily.
One of the key distinctions between local and global alignment is their definition. Local
alignment finds local regions with the highest amount of similarity between the two
sequences, whereas global alignment attempts to align the entire sequence. EMBOSS
Needle and Needleman-Wunsch Global Align Nucleotide Sequences are two alternative
techniques for global alignment. BLAST, EMBOSS Water, and LALIGN, on the other
hand, are applications for local alignment. Global alignment serves the purpose of
containing all letters from both the query and target sequences. It aligns a substring of
the query sequence to a substring of the target sequence for local alignment. Global
, alignments are commonly used to compare homologous genes, such as two genes that
perform the same function or two proteins that perform the same function. Local
alignment, on the other hand, is used to detect conserved patterns in DNA sequences,
as well as conserved domains or motifs in two proteins.
ClustalW is a tool for quickly aligning numerous nucleotide or protein sequences. It
employs progressive alignment methods, in which the most similar sequences are
aligned first, followed by the least similar sequences, until a global alignment is
achieved. T-Coffee and Dialign are consistency-based methods, whereas ClustalW is a
matrix-based approach. ClustalW provides a reasonably efficient algorithm that
outperforms other software. To calculate a global alignment, this program requires three
or more sequences. Between sequences, BLAST discovers regions of local similarity.
The program compares nucleotide or protein sequences to databases of sequences
and estimates their statistical significance. BLAST may be used to infer functional and
evolutionary links between sequences, as well as identify gene family members.
Procedure:
A. CLUSTALW
1. Open the web browser and type https://www.ebi.ac.uk/Tools/msa/clustalw2/.
2. Upload the sequences from the Notepad or paste the sequences in FASTA format.
3. Upload two sequences for pairwise alignment or more than two sequences for
multiple sequences alignment. After uploading, choose the “Execute Multiple Alignment”
option in the alignment icon.
4. Sequence alignment results will be appeared within few seconds after execution.
5. Report the result.
B. BLAST
1. Open the web browser and type http://blast.ncbi.nlm.nih.gov/Blast.cgi
2. Click either nucleotide blast or protein blast icon according to the requirement.
3. Select “Align two or more sequences” check box for opting multiple sequence
alignment or deselect for pairwise alignment.
4. Upload or paste a query sequence (in FASTA format) in the query box and execute
BLAST for pairwise alignment. This will be identifying most similar sequences from the
databank.
