Sequence analysis

In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome, transcriptome or proteome of an organism, and can also involve only selected segments or regions, like tandem repeats and transposable elements. Methodologies used include sequence alignment, searches against biological databases, and others.^[1]

Since the development of methods of high-throughput production of gene and protein sequences, the rate of addition of new sequences to the databases increased very rapidly. Such a collection of sequences does not, by itself, increase the scientist's understanding of the biology of organisms. However, comparing these new sequences to those with known functions is a key way of understanding the biology of an organism from which the new sequence comes. Thus, sequence analysis can be used to assign function to coding and non-coding regions in a biological sequence usually by comparing sequences and studying similarities and differences. Nowadays, there are many tools and techniques that provide the sequence comparisons (sequence alignment) and analyze the alignment product to understand its biology.

Sequence analysis in molecular biology includes a very wide range of processes:

1. The comparison of sequences to find similarity, often to infer if they are related (homologous)
2. Identification of intrinsic features of the sequence such as active sites, post translational modification sites, gene-structures, reading frames, distributions of introns and exons and regulatory elements
3. Identification of sequence differences and variations such as point mutations and single nucleotide polymorphism (SNP) in order to get the genetic marker.
4. Revealing the evolution and genetic diversity of sequences and organisms
5. Identification of molecular structure from sequence alone.