Bioinformatics tools

Bioinformatics tools are software programs that are designed for extracting the meaningful information from the mass of molecular biology / biological databases & to carry out sequence or structural analysis.

An example of bioinformatics is the use of computer analysis on the Human Genome Project, which has recorded the three billion basic pairs of the human DNA system.

Apart from analysis of genome sequence data, bioinformatics is now being used for a vast array of other important tasks, including analysis of gene variation and expression, analysis and prediction of gene and protein structure and function, prediction and detection of gene regulation networks, simulation environments.

The data problems such as representation (graphics), storage and retrieval (databases), analysis (statistics, artificial intelligence, optimization, etc.) and biology problems such as sequence analysis, structure or function prediction, data mining, etc.

Bioinformatics has a broader range of applications, as it deals less with the actual scientific advances, more on calculation. Simple answer is Bioinformatics, though Biotech is where a lot of groundbreaking work gets done.

The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such “bioprospecting” requires a suite of sophisticated bioinformatics tools to make sense of the data. This review summarizes the most commonly used bioinformatics tools for the assembly and annotation of metagenomic sequence data with the aim of discovering novel genes.

BLAST (Basic Local Alignment Search Tool) is one of the most widely used tools to gain sequence information. Finding similarity between DNA and protein sequences against a database is one of the first things people do when trying to get immediate information about a sequence of interest. Doing these searches allows scientists to gain knowledge about that particular gene’s function. BLAST finds regions of similarity between the input sequence and sequences found in its databases. The program compares nucleotide or protein sequences to sequence databases and then calculates the statistical significance of matches. Doing this search allows scientists to infer functional and evolutionary relationships between sequences and helps identify members of the gene family. BLAST makes use of heuristics to help provide the user with the sequence information quickly. This process occurs through a “speed-read” over similar nucleotides in the respective database. How specific these searches are can be adjusted to the user's desires.

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Nicola B
Editorial Team
Journal of  Biochemistry and Biotechnology