Bioinformatics Approaches for Gene Finding

Authors(2) :-Mahin Ghorbani, Hamed Karimi

Gene finding as process of identification of genomic DNA regions encoding proteins , is one of the important scientific research programs and has vast application in structural genomics ,functional genomics ,metabolomics, transcriptomics, proteomics, genome studies and other genetic related studies including genetics disorders detection, treatment and prevention .It is prominent that for study of all above mentioned research programs , identification of fundamental and essential elements of genome such as functional genes, intron, exon, splicing sites, regulatory sites, gene encoding known proteins, motifs, EST, ACR, etc are formed principle basis of the studies and these functions are employed by gene prediction or finding process. So gene finding process plays significant role in the study of genome related programs. Several methods are available for gene finding such as laboratory based approaches, feature based approaches homology based approaches, statistical and HMM based approaches. In this paper, we aim to discuss Insilco approaches for gene prediction in order to make scientist familiar with available bioinformatics tools for gene finding to take benefit from their advantages including low in cost, rapid in time, high in accuracy and large in scale.

Authors and Affiliations

Mahin Ghorbani
Department of Biotechnology, Fergusson College, F.C. Road, Pune, Maharashtra, India
Hamed Karimi
Department of Information Technology, Payam noor university of Farokh-shahr , Farokh-shahr, Chaharmahl va bakhtiari, Iran

Gene finding, Gene prediction, bioinformatics tools, genome study, Insilco approaches.

  1. Rastogi .S. C., Rastogi P and Mendiratta N., 2008. Bioinformatics Methods and Applications: Genomics .Proteomics And Drug Discovery PHI Learning Pvt. Ltd
  2. Korf I. (2004-05-14). "Gene finding in novel genomes". BMC Bioinformatics 5: 59–67.
  3. Neelam Goel, Shailendra Singh, Trilok Chand Aseri (2013). "A comparative analysis of soft computing techniques for gene prediction". Analytical Biochemistry. doi:10.1016/j.ab.2013.03.015.
  4. Mathé C, Sagot MF, Schiex T, Rouzé P. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 2002 Oct 1;30(19):4103-17.
  5. Uberbacher EC, Hyatt D, Shah M.GrailEXP and Genome Analysis Pipeline for genome annotation. Curr Protoc Hum Genet. 2004 Feb;Chapter 6:Unit 6.5. doi:10.1002/0471142905.hg0605s39.
  6. Sequencher® version 5.3 sequence analysis software, Gene Codes Corporation, Ann Arbor, MI USA http://www.genecodes.com
  7. Neena Haider. Biotech Software & Internet Report. November 2000, 1(5): 208-213. Doi: 10.1089/152791600750034730.
  8. Fickett JW.Recognition of protein coding regions in DNA sequences. TEST CODE Nucleic Acids Res. 1982 Sep 11; 10(17):5303-18.
  9. Lukashin A. and Borodovsky M. "GeneMark.hmm: new solutions for gene finding." Nucleic Acids Research (1998) 26 (4): 1107–1115.
  10. Anders Krogh.Using Database Matches with HMMGene for Automated Gene Detection in Drosophila. Genome Res. 2000 Apr; 10(4): 523–528.
  11. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER, Nucleic Acids Research 27:23 (1999), 4636-4641.
  12. Salzberg S, Delcher A, Kasif S, White O. Microbial gene identification using interpolated Markov models, Nucleic Acids Research 26:2 (1998), 544-548.
  13. Dong, S. and Searls, D.B."Gene Structure Prediction by Linguistic Methods" (1994) Genomics 23:540-551.
  14. Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T (2005)MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 21, 2933-42.
  15. Cartharius K (2005) MatInspector: Analysing Promoters for Transcription Factor Binding Sites in "Analytical tools for DNA, genes and genomes: nuts & bolts", by Arseni Markoff ed., The nuts & bolts series, DNA Press, 2005, ISBN 0-9748765-1-8.
  16. Jun Ishikawa* and Kunimoto Hotta .FramePlot: a new implementation of the Frame analysis for predicting protein-coding regions in bacterial DNA with a high G+C content.FEMS Microbiology Letters Volume 174, Issue 2, pages 251–253, May 1999.
  17. Ghorbani M ,Karimi H ,Ten Bioinformatics Tools for Single Nucleotide Polymorphisms , American Journal of Bioinformatics ;2014:3(2):45-48
  18. Ghorbani M and Karimi H. Cyclin-Dependent Kinases as valid targets for cancer treatment. Journal of Pharmacy Research 2015,9(6),377-382
  19. Ghorbani M , Karimi H , 'Ion Channels Association with Diseases and their Role as Therapeutic Targets in Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):65-69,July-August 2015.
  20. Ghorbani M , Karimi H , 'Role of Aquaporins in Diseases and Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST),1(3):60-64, July-August 2015
  21. Ghorbani M, Karimi H, 'Role of Microarray Technology in Diagnosis and Classification of Malignant Tumours', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):117-121, July-August 2015
  22. Mahin Ghorbani, Hamed Karimi, 'Role of G-Protein Coupled Receptors in Cancer Research and Drug Discovery', International Journal of Scientific Research in Science and Technology (IJSRST),1(3), pp.122-126 , July-August 2015.
  23. Mahin Ghorbani, Hamed karimi, 'Role of Biomarkers in Cancer Research and Drug Development', International Journal of Scientific Research in Science and Technology(IJSRST),1(3), pp.127-132, July-August 2015

Publication Details

Published in : Volume 1 | Issue 4 | September-October 2015
Date of Publication : 2015-10-25
License:  This work is licensed under a Creative Commons Attribution 4.0 International License.
Page(s) : 12-15
Manuscript Number : IJSRST15143
Publisher : Technoscience Academy

Print ISSN : 2395-6011, Online ISSN : 2395-602X

Cite This Article :

Mahin Ghorbani, Hamed Karimi, " Bioinformatics Approaches for Gene Finding ", International Journal of Scientific Research in Science and Technology(IJSRST), Print ISSN : 2395-6011, Online ISSN : 2395-602X, Volume 1, Issue 4, pp.12-15, September-October-2015.
Journal URL : https://ijsrst.com/IJSRST15143
Citation Detection and Elimination     |      | | BibTeX | RIS | CSV

Article Preview