Rajdeep Singh
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Rajdeep Singh


What is a Sequence alignment?

Sequence alignment helps to compare DNA, RNA, and Protein

Sequence alignment
Photo by National Cancer Institute on Unsplash

Sequence alignment is a method used in bioinformatics. You use the Sequence alignment tool to compare two DNA or RNA and also protein. base on compare you check the

  1. difference between two DNA or RNA and Protein.
  2. You also check Mutation inside the cell.
  3. You create a molecule 3d structure.
  4. You compare DNA or RNA from other species.
  5. You design your own new Drug.
  6. You build your own AI computer model base on biological data

Definition of Sequence alignment

Sequence alignment is the process of comparing and detecting similarities between biological sequences (DNA, RNA, and Protein).


Sequence analysis is the method of comparing nucleotide and protein sequences in which we intend to find identical or similar sequence characters in the same column.

In This Article, we cover basic information about Sequence alignment. If you learn more, then follow our reference.


Sequence alignment

Two types of Sequence alignments

  • According to the sequence number
  • According to the sequence length

According to the sequence number

  1. Pairwise sequence alignment (PSA)
  2. Multiple sequence alignment (MSA)

Pairwise sequence alignment (PSA)

In pairwise sequence alignment, we compare only two sequences to find the region of similarity or dissimilarity. It also helps to find the evolution of the sequence.

Pairwise sequence alignment
Pairwise sequence alignment

Multiple sequence alignment (MSA)

In Multiple sequence alignment, we compare more than two sequences to find out gene families, protein families, enzyme active site, functional and evolutionary relatedness, etc.

Multiple sequence alignment example
Multiple sequence alignment example

According to the sequence length

  1. Global sequence alignment
  2. Local sequence alignment

Global sequence alignment

In global alignment, sequences are aligned/compared along their entire length to include as many matching characters as possible. sequences of almost equal length serve as a good candidate for global alignment

Global sequence alignment example
Global sequence alignment example

Local sequence alignment

In local alignment, sequences are alignment to find regions of higher density or strong similarity.

Local sequence alignment example
Local sequence alignment example


  1. Positions at which a letter is paired with a null are called gaps.
  2. Gap scores are typically negative.
  3. Gap denoted by “-” chartered.
Gaps in gene Example
Gaps Example

Best Tool or Software to Sequence alignment tool

Two tools right now commonly use in bioinformatics first is BLAST and the second is FASTA, and the last one is GeneWise.

But I recommend you search for more tool software that is open-source and try to play with it.


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Computer Science & Biology & Bioinformatic

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Rajdeep singh

Rajdeep singh

JavaScript || Python || Rust || Biotechnology || Bioinformatic || Front-end Developer || https://officialrajdeepsingh.dev/

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