Bioinformatics

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This document contains preface.

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It is the cell that makes an organism living in all living organisms. Each and every organism is made up of cells, either single celled or multiple celled. The organisms which have a single cell in them are called unicellular organisms and those organisms which are made up of many cells are called multi-cellular organisms.

Bioinformatics in its simplest form can be defined in a single sentence as “It is the intersection of biology and Information Technology”. Or we may state it as “It is the science of using Information Technology to understand Biology”.

Public Biological Databases have been developed to hold the enormous molecular biology data. These databases are established for the scientists across the world to research and exchange their software and data. They are connected together with the help of the WWW.

The central dogma of life or the central dogma of molecular biology consists mainly of three processes, which are replication then transcription and then translation.
The central dogma of molecular biology was first described by James Watson. He said, the process of replication duplicates DNA, the process of transcription converts a DNA into RNA and the process of translation converts RNA into proteins.

DNA is a helix with a width of 2 nanometer . The bases are positioned one above the other at a distance of 0.34 nm in a form of steps. The steps make a full turn at a length of 3.4 nanometer. Therefore, at least ten base layers need to be located in one turn of DNA.

The proteins function through chemical reactions, which are carried out with the help of amino acids and small organic molecules called cofactors which normally attach themselves to the proteins.

The genetic material inside an organism is the DNA. This is also the hereditary material which is passed from one generation to the other. The development and multiplication of an organism is dependent on the DNA. We resemble our parents and grandparents in having similarities such as, our mother’s blue eyes, our father’s brown hair, our grandmother’s short height, our grandfather’s big ears.

Sequences are compared by aligning them together and then finding the differences among them.
There may be single sequence alignments or multiple sequence alignments. Sequence comparison is mostly done of nucleic acids, proteins and RNAs. There are a number of algorithms which are used to do this and dynamic programming method is an advancement over the others. In comparing two sequences their distance and similarity is noted. The gaps are found out. Then pairwise alignments can be done or matrices can be formed to find out the scores. BLAST and FASTA are used for database searches, we will be discussing all the points related to sequence comparison in the following sections.

Perl is a programming language which is most popular for the Bioinformatics data. It is easy and simple to use and is particularly helpful in handling the data used in bioinformatics.

In the field of Bioinformatics you would require to change the format of the data to keep it consistent with data collected from other sources. So the software which most suits these needs are available in the Perl language.

This document contains the index.