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Sequence Alignment & Analysis

Updated: Apr 1, 2021

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

  • Database Searching

  • Secondary structure prediction of proteins from mere its sequence

  • Comparative genomics analysis

  • Functional Proteomics

  • Biological Data Annotations

  • Phylogenetic analysis

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.

Bioinfolytics & Our Services

If you want to learn and develop your expertise in Sequence Alignment and Analysis or if you’ve any research project that requires such services, join our Gray Bioinformatics plans from BioCode, where we’re providing you with complete video lectures on the databases and the tools that are required for this purpose and teach you how to analyze the results and draw logical conclusions and hypothesis from the results.

To join our Gray Bioinformatics plans, visit us at and enroll yourself to develop your skills in Bioinformatics databases and tools at affordable costs.

BioCode through BioinfoLytics, is providing its services for the analysis of your query DNA/RNA and protein sequences, alignment of two or more query sequences, prediction and analysis of evolutionary conserved regions of proteins (motifs & domains) and the secondary structure prediction of proteins.

Through BioinfoLytics, we’re providing our expertise to align, analyze and deduce possible conclusions from the query sequences provided by the users, in a very efficient and professional manner within a reasonable price. The user just has to provide the query sequences and the type of analyses he/she wants to be done on the sequences, and before the deadline he/she will be provided with the results for further analysis.

We’ll be delighted to provide you our platform of BioinfoLytics, where you can sell your skills as a freelancer.

For further information on our services, visit us at

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