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Bioinformatics: Bioinformatics is the
anch of science in which using the computational tools biological data is analyzed and interpreted. It is a multi-disciplinary field, which connects different
anches like physics, computer science, biology and mathematics together [1].
Basic principles utilized in the Bioinformatics technology:
The basic principles utilized in the Bioinformatics technology are discussed as below:
1. Retrieval of the sequence of interest and the desired manipulation – To achieve this, firstly the sequence of interest is searched in all databases or particularly the nucleotide sequences are searched in the drop-down list at the National Center for Biotechnology Information (NCBI) via the search engine “Entrez”. Search is made with the help of suitable keywords, accession number of gene, name of gene or name of species and the search results will provide the list of genes, related sequences, proteins etc. displayed mostly in FASTA [2].
2. Sequence alignment- Sequence alignment is very essential for the purpose of search and assembly of sequence and for phylogenetics. It is commonly performed by the open access softwares- Bio-Edit and MEGA which are freely downloadable and can gets installed easily. For alignment purpose, sequences saved in FASTA format are used as an input and aligned by means of the ClustalW program [3].
3. Phylogenetics- Phylogenetic examination is used for the taxonomical, systemic and evolutionary analysis of the gene sequence. In this, multiple sequences are clustered according to the genetic distances using the software MEGA and a phylogeny tree is constructed [4].
4. Similarity search-To understand the evolutionary relationship between different genes, sequence comparison is performed via the resemblance search tool – BLAST or the Best Local Alignment Search Tool provided by NCBI and European Bioinformatics Institute (EBI). Through BLAST, the nucleotide or protein sequence to be studied is compared with all the all of the accessible sequence databases [5].
5. Primer design- Primer designing is an essential step of marker development like simple sequence repeats markers and is performed via PRIMER 3.0 [6].
6. Advanced Skills- The advanced skills of bioinformatics comprise the designing of databases and specific algorithms for the purpose of multiple sequence alignment and their analysis. Along with this, the annotation of several kinds of oligonucleotide chips, mass spectrometry, microa
ays, and varied stages of next-generation sequencing [7,8].
To convince Holien-X, the chosen method along with its pros and cons is discussed as below: The best technique to sequence the desired nucleotide data is the “Next generation sequencing”. This is the best method for large-scale gene sequencing of diseased genes for research and diagnostics. Next-generation sequencing (NGS) is an enormously equivalent sequencing technology which provides the ultra-high output. It is scalable, and has very high speed. This technology is castoff for the determination of order of nucleotides in the entire genomes or the selected portions of DNA or RNA. The process of Next-generation sequencing enumerates the distinct digital sequencing read counts and offers a wider active range. Next Generation sequencing-based RNA-Sequencing is an influential technique that allows the investigators to go through the disorganization and disbursement of bequest skills like microa
ays. This technique has transformed the genetic sciences, consenting labs to accomplish an extensive variety of applications and learning the biological organizations at a level which was not at all possible before [9]. The Pros of this method is that it can sequence the complete Exome (Protein coding gene) or genome in an unbiased manner. It is easily available, affordable and one-step approach. The Cons of this method is that if the diseased gene is outside the...