There are data-mining software that retrieves data from genomic sequence databases and also visualization tools to analyze and retrieve information from proteomic databases.
These can be classified as homology and similarity tools, protein functional analysis tools, sequence analysis tools and miscellaneous tools.
Here is a brief description of a few of these. Everyday bioinformatics is done with sequence search programs like BLAST, sequence analysis programs, like the EMBOSS and Staden packages, structure prediction programs like THREADER or PHD or molecular imaging/modelling programs like RasMol and WHATIF.
4 Major categories of Bioinformatics Tools are:
1. Homology and Similarity Tools:
- Homologous sequences are sequences that are related by divergence from a common ancestor.
- Thus the degree of similarity between two sequences can be measured while their homology is a case of being either true of false.
- This set of tools can be used to identify similarities between novel query sequences of unknown structure and function and database sequences whose structure and function have been elucidated.
2. Protein Function Analysis:
- These groups of programs allow you to compare your protein sequence to the secondary (or derived) protein databases that contain information on motifs, signatures and protein domains.
- Highly significant hits against these different pattern databases allow you to approximate the biochemical function of your query protein.
3. Structural Analysis:
- These sets of tools allow you to compare structures with the known structure databases.
- The function of a protein is more directly a consequence of its structure rather than its sequence with structural homologs tending to share functions.
- The determination of a protein's 2D/3D structure is crucial in the study of its function.
4. Sequence Analysis:
- This set of tools allows you to carry out further, more detailed analysis on your query sequence including evolutionary analysis, identification of mutations, hydropathy regions,
- CpG islands and compositional biases.
- The identification of these and other biological properties are all clues that aid the search to elucidate the specific function of your sequence.
