Bioinformatics and Functional Genomics
Introduction
Bioinformatics is a growing revolution in the field of molecular biology and computers. Here, our emphasis will be on employing bioinformatics tools and biological databases to address challenges from current issues in biological, biotechnological, and biomedical research. Such as looking at computational algorithms and computer databases to analyze proteins, genes, and the complete collection of deoxyribonucleic acid DNA that comprises an organism or genome. A major challenge in biology currently is to analyze and ascertain insights from large quantiites of data garnered via genome-sequencing, proteomics, and other biolgical projects that yield sequencing and structural data. Therefore, there is a need for tools of bioinformatics to help reveal the fundemental, underlying strucutre and function of biological problems relating to macromolecules, biochemical pathways, disease processes, and evolution, to name a few.
Pairwise Sequence Alignment
Introduction
Two proteins relating at the sequence levels suggest they are homologous and is an important question for genes or proteins. If two genes are homologous, then they evolved from a common ancestor and suggests that they share common functionality. Thus, the motivation of developing tools to analyze many DNA and protein sequences is to identify domains or motifs that are shared among common molecules, which can be accomplished by aligning sequencing. This has many uses, one of which is to use our understanding of proteins and gene relatedness within and between organisms, to imrpove our fundemental understanding of life.
Protein Alignment
Basic Local Alignment Search Tool BLAST Algorithm
The Basic Local Alignment Search Tool BLAST Algorithm reveals what related sequences are present in the same and other organisms. At a large scale view, BLAST preforms a pairwise sequence alignment for one sequence, termed the query, and the entire database, termed the target. This results in tens of millions of sequences evaluations where the return data are matches that most closley relate. A benefit of BLAST compared to other global or local alignment algorithms is that it offers a local alignment strategy having both speed and sensitivity. In this section we will analyze the procedure for the BLAST algorithm.
The procedure for BLAST is described in the following four sequential steps: sequence of interest, BLAST selected implementation, database selection, and then parameter selection.
Sequence of Interest
BLAST Selected Implementation
Database Selection
Parameter Selection
To continue.