Sequence alignment
Sequence Alignment
Sequence alignment is a method used in bioinformatics to arrange the sequences of DNA, RNA, or protein to identify regions of similarity. These similarities may be a result of functional, structural, or evolutionary relationships between the sequences.
Pronunciation
- Sequence: /ˈsiːkwəns/
- Alignment: /əˈlʌɪnmənt/
Etymology
The term "sequence alignment" is derived from the English words "sequence" and "alignment". "Sequence" comes from the Latin word "sequentia", meaning "a following", and "alignment" comes from the French word "aligner", meaning "to line up".
Related Terms
- Multiple sequence alignment
- Pairwise sequence alignment
- Gap penalty
- Sequence assembly
- Sequence database
- Sequence homology
Description
In bioinformatics, sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships among the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the sequences to optimize the alignment and to introduce gaps in the sequences.
Sequence alignment can be used to assess similarity, to infer phylogenetic relationships, to find conserved sequences and to predict the function and structure of unknown sequences. There are two main types of sequence alignment: pairwise sequence alignment and multiple sequence alignment.
Methods
There are various methods used to perform sequence alignment. The choice of the method depends on the number of sequences to be aligned, the assumed evolutionary distance between them and the purpose of the alignment. The most common methods are:
- Dynamic programming algorithms: These are used for optimal pairwise sequence alignment. Examples include the Smith-Waterman algorithm for local alignment and the Needleman-Wunsch algorithm for global alignment.
- Heuristic methods: These are used for multiple sequence alignment. Examples include FASTA and BLAST.
Applications
Sequence alignment is used in various fields of biology. It is fundamental to the annotation of genome sequencing projects, it is used in comparative genomics, and it is central to the field of phylogenetics.
External links
- Medical encyclopedia article on Sequence alignment
- Wikipedia's article - Sequence alignment
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