The Basics of Genomics, Proteogenomics: The Demands and Roles that Proteomics can Fulfil in Genome Annotation

Authors

  • Harshita Yadav Student, Department of Botany, Harish Chandra Post Graduate College, Varanasi, Uttar Pradesh, India

Keywords:

DNA sequences, Eukaryotic, Genomics, Genome annotation, Database

Abstract

The science of genomes: scientists have only recently gone from analysing a few or a limited number of genes at a time to investigating thousands of genes, moving from the study of inheritance units to the investigation of an organism's entire genome. The science of genomes, or "genomics," was originally focused to determining DNA sequences (the nucleotide order on a specific fragment of DNA), but it quickly evolved to a more functional level—studying gene expression profiles and roles. The purpose of this chapter is to review the basic assumptions and definitions that underpin genomics, as well as to clarify essential concepts and methodologies that genomics rely is based on.

 

References

Parra, G., Blanco, E. and Guigó, R., 2000. Geneid in drosophila. Genome research, 10 (4), pp. 511–515.

Meyer, I.M. and Durbin, R., 2004. Gene structure conservation aids similarity based gene prediction. Nucleic acids research, 32 (2), pp. 776–783.

Pavy, N., Rombauts, S., Dehais, P., Mathe, C., VV Ramana, D., Leroy, P. and Rouze, P., 1999. Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics, 15 (11), pp.887–899.

Guigó, R., Knudsen, S., Drake, N. and Smith, T., 1992. Prediction of gene structure. Journal of molecular biology, 226 (1), pp.141–157.

Burge, C. and Karlin, S., 1997. Prediction of complete gene structures in human genomic DNA. Journal of molecular biology, 268 (1), pp.78–94.

Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M. and Louis, E.J., 1996. Life with 6000 genes. Science, 274 (5287), pp. 546–567.

7.Peterson, J.D., Umayam, L.A., Dickinson, T., Hickey, E.K. and White, O., 2001. The comprehensive microbial resource. Nucleic acids research, 29 (1), pp. 123–125.

Meyer, F., Goesmann, A., McHardy, A.C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R. and PuÈhler, A., 2003. GenDB—an open source genome annotation system for prokaryote genomes. Nucleic acids research, 31 (8), pp. 2187–2195.

Van Domselaar GH, Stothard P, Shrivastava S, et al. BASys: a web server for automated bacterial genome annotation, Nucleic Acids Res, 2005, vol. 33 (pg. W455–9)

Delcher, A.L., Harmon, D., Kasif, S., White, O. and Salzberg, S.L., 1999. Improved microbial gene identification with GLIMMER. Nucleic acids research, 27 (23), pp. 4636–4641.

Salzberg, S.L., Delcher, A.L., Kasif, S. and White, O., 1998. Microbial gene identification using interpolated Markov models. Nucleic acids research, 26 (2), pp. 544–548.

Badger, J.H. and Olsen, G.J., 1999. CRITICA: coding region identification tool invoking comparative analysis. Molecular biology and evolution, 16 (4), pp. 512–524.

Altschup, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J., 1990. Basic local alignment search tool. J Mol Biol, 215 (3), pp. 403–10.

Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, 1997, vol. 25 (pg. 3389–402)

15Gish, W. and States, D.J., 1993. Identification of protein coding regions by database similarity search. Nature genetics, 3 (3), pp. 266–272.

16. Tatusov, R.L., Koonin, E.V. and Lipman, D.J., 1997. A genomic perspective on protein families. Science, 278 (5338), pp. 631–637.

Haft, D.H., Loftus, B.J., Richardson, D.L., Yang, F., Eisen, J.A., Paulsen, I.T. and White, O., 2001. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic acids research, 29 (1), pp. 41–43.

Ansong, C., Purvine, S.O., Adkins, J.N., Lipton, M.S. and Smith, R.D., 2008. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Briefings in Functional Genomics and Proteomics, 7 (1), pp. 50–62.

Downloads

Published

2022-03-12

Issue

Vol. 10 No. 3 (2021)

Section

Review Article

License

Declaration and Copyright Transfer Form

(to be completed by authors)

I/ We, the undersigned author(s) of the submitted manuscript, hereby declare, that the above manuscript which is submitted for publication in the STM Journals(s), is not published already in part or whole (except in the form of abstract) in any journal or magazine for private or public circulation, and, is not under consideration of publication elsewhere.

  • I/We will not withdraw the manuscript after 1 week of submission as I have read the Author Guidelines and will adhere to the guidelines.
  • I/We Author(s ) have niether given nor will give this manuscript elsewhere for publishing after submitting in STM Journal(s).
  • I/ We have read the original version of the manuscript and am/ are responsible for the thought contents embodied in it. The work dealt in the manuscript is my/ our own, and my/ our individual contribution to this work is significant enough to qualify for authorship.
  •  I/We also agree to the authorship of the article in the following order:

Author’s name                                    

 

1. ________________

2. ________________

3. ________________

4. ________________

 

We  Author(s) tick this box and would request you to consider it as our signature as we agree to the terms of this Copyright Notice, which will apply to this submission if and when it is published by this journal.