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tools and Software of Bioinformatics

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Abstract

Bioinformatics is the field was not so much known in the past. With the passage of time science has been progressed. As the science progressed there are many fields of the science has been merged and give rise the new fields. Bioinformatics is the new field I the science. It has not very well scope in Pakistan but it is very important field in the other countries. This field is working with the other fields like computer, math, state, and molecular biology etc. This field is growing field and its progress is very fast. Within the 15 month its data has been doubled. People use online tools to study the sequence of the protein and nucleic acid. It help in the finding of the amino acid sequence.

There are many challenges of the data in the field of the biology. All the data of the biology has been computerized. This data is usually related to the molecular biology. This data help in the study of the gene expression, genomics and proteomics. In this review we will discuss the tools of the bioinformatics. Tools are the online software which helps in the search of the proteomics and genomic. It is the summary of the tools we will discuss later them one by one in detail and also will be known about their function. These tools provide us the 3d structure of the biomolecules. That tool provides us the useful information of the biological data. These tools included Genbank, ENTREZ, iTASSER, GENSCAN, ORF finder, Modeller, EMBL, Expasy, READSEQ and Magpie will be discuss in detail in the review. These tools are very specific in their function, input and output. These tools design as the new data can be input in them and the information can be get from the present data. Introduction Bioinformatics is online tools used to study the organism’s molecules. This field is merged with computer, mathematics, biology and many other fields. In very beginning, there is a lot of data has been collected but human memory is not very efficient to remember all the data. So it decided computerize all the data. There are many online tools are available to collect the data. With the help of these tools we can search about the proteins sequence, nucleic acid sequence and amino acid sequence. Bioinformatics is the study of biological molecules sequence by using the online tools. It is very important to find the sequence of the proteins.

We can study the genetic disease which is replaced by the normal amino acid. It is very useful field in the medicine, medical, surgery and research field. Bioinformatics reveals the study of proteins and genes with very other aspects. The study of the protein is called proteomics and the study of the genes is called genomics bioinformatics provides us 3D structure of the protein, genome amino acids etc. Data is stored by the using the online tools. It is also analysis the data. When we have new data we will input it into the tool it will provide us the information about it. New structures can be finds through these tools. it is very fast growing field has many application in the future. It help in the medical field. It has many applications in the research and medical field.

Genbank Gene bank is a online tool which help in the finding of the gene finding. It is the NIH genetic sequence database. There is a collection of all publicly available of DNA sequences [1] Gene bank is release in 194, produced in February 2013. It contained over 150 billion nucleotide bases in more than 162 million sequences [2].Genbank database includes extra data sets that are made mechanically from the main sequence data collection, and therefore are excluded from this count [2]. Specificity Gene bank contains the information of the genes including plants and animal. It contains many databases. It has the specialty of the gene and proteins. It is directly involve in the submission of the bulk of the database. It is very important to submit the data as whole. Function: It open the sequence of the selective gene.

Entrez It is the NCBI basic search tools and retrieval system. It has many biomedical literatures. It contains data of DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. It is text base search. Entrez is an indexing and retrieval database. It is grouped data base. it is widely use in the health sciences and biotechnology [3]. Specificity: It is text based tools and research engine for protein and genes. It is specify for the entrez information of the gens and proteins. Function: It help in the bio project It help in the bio sample It work with the genbank and NCBI It provides the information about the genes and proteins. It provide the genes entrez, iTASSER: Iterative Threading Assembly Refinements is the online tool in the bioinformatics. This help in the predicting the three dimension structure of the proteins from the amino acids [3] Specificity: Through threading technique, it predicts the structure of the templates with the help of Protein Data Bank. It constructs the full length structure from the resembling structural fragments of the templates. It can be downloads from website. Function It allow to it user to provide the structure information of the structure of the protein. It provides the information of the Ligand Binding site. Go term and the confident sore. It also help in the B factor estimation. Top 10 proteins in the database help in the prediction of the unknown structure. Cluster density help in the top 5 full length ranked. It is also help in the distance mapping.

ORF Finder Open reading frames (ORFs) in the DNA sequence is find out through this engine. ORF finder is used to search newly sequenced DNA for potential protein encoding segments to verify predicted protein using newly developed SMART BLAST or regular BLASTP[4] The web design of the ORF finder is limited to the sub range of the query sequence up to 50 kb long[5]. The program returns the range of each ORF, along with its protein translation. SPEIFICITY It has ability to read the open frame which is translated. This is the online tool use for the search of the start codon for the stretched[6] Function: It is very important to find the open reading frame on the DNA To find the start codon. It helps in the finding of the ORF on the amino acid. ORF encoded by the genes.

BLAST (Basic Local Alignment Search Tool) comes under the category of homology and similarity tools. It is a set of search programs designed for the Windows platform and is used to perform fast similarity searches regardless of whether the query is for protein or DNA. Comparison of nucleotide sequences in a database can be performed[7] Also a protein database can be searched to find a match against the queried protein sequence. NCBI has also introduced the new queuing system to BLAST (Q BLAST) that allows users to retrieve results at their convenience and format their results multiple times with different formatting options[8]. Depending on the type of sequences to compare, there are different programs: 1)blastp compares an amino acid query sequence against a protein sequence database 2)blastn compares a nucleotide query sequence against a nucleotide sequence database 3)blastx compares a nucleotide query sequence translated in all reading frames against a protein sequence database 4)blastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames 5)blastx compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database

EMBOSS (European Molecular Biology Open Software Suite) is a software-analysis package. It can work with data in a range of formats and also retrieve sequence data transparently from the Web.[9] Extensive libraries are also provided with this package, allowing other scientists to release their software as open source. It provides a set of sequence-analysis programs, and also supports all UNIX platforms. Clustalw: It is a fully automated sequence alignment tool for DNA and protein sequences. It returns the best match over a total length of input sequences, be it a protein or a nucleic acid. RasMol: It is a powerful research tool to display the structure of DNA, proteins, and smaller molecules. Protein Explorer, a derivative of RasMol, is an easier to use program

COPIA (COnsensus Pattern Identification and Analysis) is a protein structure analysis tool for discovering motifs (conserved regions) in a family of protein sequences. Such motifs can be then used to determine membership to the family for new protein sequences, predict secondary and tertiary structure and function of proteins and study evolution history of the sequences. Actually it's depend on the area which you want to do work either the tools are present or you have to create for that matter using different programming languages, Like Perl, JAVA, Python etc.

FAST homology search All sequences .An alignment program for protein sequences created by Pearson and Lipman in 1988. The program is one of the many heuristic algorithms proposed to speed up sequence comparison[10 The basic idea is to add a fast prescreen step to locate the highly matching segments between two sequences, and then extend these matching segments to local alignments using more rigorous algorithms such as Smith-Waterman

PROSPECT Protein Structure Prediction and Evaluation Computer Tool Kit is a protein-structure prediction system that employs a computational technique called protein threading to construct a protein's 3D model. PatternHunter :PatternHunter, based on Java, can identify all approximate repeats in a complete genome in a short time using little memory on a desktop computer. Its features are its advanced patented algorithm and data structures, and the java language used to create it. The Java language version of PatternHunter is just 40 KB, only 1% the size of Blast, while offering a large portion of its functionality

Conclusion

Bioinformatics is a very important field in the biology. It is developing files. Online tools access to the every person. It has great importance in the research. Publically available websites are the most important. All of the tools has their own importance and design for a specific purpose. Clinical research is making toiling efforts for promotion and wellbeing of the health status of the people. There is a rapid increase in number and severity of diseases like cancer, hepatitis, HIV etc, resulting in high morbidity and mortality. Clinical research involves drug discovery and development whereas clinical trials are performed to establish safety and efficacy of drugs. Drug discovery is a long process starting with the target identification, validation and lead optimization. This is followed by the preclinical trials, intensive clinical trials and eventually post marketing vigilance for drug safety. Softwares and the bioinformatics tools play a great role not only in the drug discovery but also in drug development. It involves the use of informatics in the development of new knowledge pertaining to health and disease, data management during clinical trials and to use clinical data for secondary research. In addition, new technology likes molecular docking, molecular dynamics simulation, proteomics and quantitative structure activity relationship in clinical research results in faster and easier drug discovery process.

References

1. Benson D; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Wheeler, D. L.; et al. (2008). GenBank . Nucleic Acids Research. 36 (Database): D25 D30. PMC 2238942  PMID 18073190.

2. Ostell, J. 2002. The Entrez search and retrieval system. IN The NCBI handbook [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, Chapter 14. Available from the Entrez Books database

3. U.S. National Library of Medicine. 2015-10-19. Retrieved 2015-10-22.

4. Jump up Slonczewski, Joan; John Watkins Foster (2009). Microbiology: An Evolving Science. New York: W.W. Norton & Co. ISBN 978-0-393-97857-5. OCLC 185042615.

5. Jump up to:a b c d Deonier, Richard; Simon Tavaré; Michael Waterman (2005). Computational Genome Analysis: an introduction. Springer-Verlag. p. 25. ISBN 0-387-98785-1

6. Kuratani, M., et al., 2006. Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea. Journal of Molecular Biology 355: 395-408.

7. Garrett, R. H., Grisham, C. M., 2013. Biochemistry. Chapter 30: Protein Synthesis in Biochemistry (pp.1050), 5th ed. Canada: Brooks/Cole, Cengage Learning.

8. Pratas, D.; Hosseini, M.; Pinho, A. (2017). Cryfa: a tool to compact and encrypt FASTA files . 11'th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB), Springer: 305 –312.

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