Biomolecules such as DNA, RNA and proteins are made up of their subunits (amino acid or nucleotide residues). The sequence of such residues determines the structures and functions of the biomolecules. Hence, to analyze and predict the structures and functions of any protein or DNA/RNA, it’s important to analyze its sequence first. Sequence Alignment refers to the process of comparing two or more sequences to find out the regions of higher similarity or evolutionary conserved regions between the query sequences.
Sequence Alignment and Analysis is the core of many Bioinformatics applications and analyses and to extract the substantial amount of information from these sequence alignments special skills are required from the analytics.
Sequence analysis refers to computational analysis of the sequences of amino acids or nucleotide residues to extract the knowledge about the properties, structure, biological functions and evolutionary diversity of proteins or DNA/RNA molecules, respectively.
Sequence analysis can be done for:
The analysis of Aligned sequences
Domain & Motif analysis
Secondary structure prediction of proteins from mere its sequence
Comparative genomics analysis
Biological Data Annotations
Types of Sequence Alignment
On the basis of numbers of sequences to be aligned, sequence alignment is of two types:
Pairwise sequence alignment- Alignment of two sequences.
Multiple sequence alignment- Alignment of more than 3 sequences.
On the basis alignment algorithms, it can be divided into:
Local Alignment- the regions of higher similarity are aligned, sometimes by the addition of gaps. It aims in searching similarities in large sequences and identifying conserved regions (Domains & Motifs) with two proteins.
Global Alignment- aligning the sequences across their entire lengths and the terminating ends of the sequences are aligned first. This method assumes two sequences as potentially equivalent and aims in identifying conserved regions and differences among query sequences.
How Sequence Alignment Further Facilitates the Analysis
After aligning the sequences, the results are subjected to further analysis to draw possible inferences, such as if the query sequences are homologous or not, the identification of intrinsic properties of sequences (PTMs, regulatory elements, active site residues, reading frames, etc.), identification of point mutations (SNPs, Microsatellite and other genetic markers, etc), exploring the evolutionary genetic diversity of query sequences, and prediction of molecular structure from the sequence alone.
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