Bioinformatics Softwares


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Introduction

Bioinformatics and computational biology (sometimes called systems biology) involve the use or
development of techniques, including applied mathematics, informatics, statistics, computer science,
artificial intelligence, chemistry, and biochemistry to solve biological problems, usually on the
molecular level. The primary goal of bioinformatics is to increase our understanding of biological
processes. It is different from other approaches because of its focus on developing and applying
computationally intensive techniques to achieve this goal. Major research efforts in the field include
sequence alignment, gene finding, genome assembly, protein structure alignment, protein
structure prediction, prediction of gene expression and protein-protein interactions, and the modeling
of evolution. Most of the Bioinformatics algorithm deals with very large sequences of DNA or
Proteins. Maintaining and processing of such large sequences have high storage and computational
complexity.

Databases

At the basic level, bioinformatics was used to organize biological data to help the researcher’s access
information, add and modify new information. The key was to make the biological information
available for analysis and developing applications. The approximate classification is :
• Protein Databases
• Structural Databases
• Nucleotide and Genome Sequences Databases
• Others

Protein Databases

Life depends on 3 critical molecules and one of them is protein. Primary protein databases contain
over 300,000 protein sequences that function as a repository for raw data.

Conclusion

My project was to explore open source tools (Specially BioJava) so that any bioinformatics related
algorithmic problem can be mapped and solved using it. I explore it little and discover some bioinformatics
algorithm implementation in BioJava. Moreover I started implementing a library based
on the algorithm we studied in this course. I already implemented Partial Digest Problem and Motif
Finding in Java. The source codes are given in the appendix.