How to obtain the nucleotide sequences DNA from gene bank data base
Keywords:
NCBI, contig, mRNA, CDS, nucleotide sequences, introns, exons
Abstract
A method of extraction nucleotide sequences of human mRNA from Gene Bank flat format of NCBI was proposed. The method is based on using regular expressions PERL language on the basis of Extended Backus–Naur Forms (EBNF). Suggested for work set of regular expressions could be used for the analysis of other genomes' sequences that are presented in Gene Bank flat format (gbk).
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References
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15. Пат. 43786 Україна, МПК (2007) G 06 F, 17/21. Спосіб перетворення структури послідовностей генів бази даних / Дуплій Д.Р., Калашніков В.В., Чащин Н.А., заявник та патентовласник Київ. Ін-т Молекулярної Біології и Генетики; Держ.реєстр. від 25.08.09.
2. Cochrane G. R., Galperin M. Y. The 2010 Nucleic Acids Research Database Issue and online database collection: a community of data resources // Nucl. Acids Res. – 2010.– V.38.– D1-D4; doi:10.1093/nar/gkp1077.
3. Sayers E. W., Barrett T., Benson D. A. [et al.]. Database resources of the National Center for Biotechnology Information // Nucl. Acids Res. – 2010.– V. 38.– D5-D16; doi:10.1093/nar/gkp967.
4. The NCBI C++ Toolkit [Internet] / edit. Vakatov D., Siyan, K., Ostell J. – Bethesda (MD): National Library of Medicine (US), NCBI; 2004.
5. Gilat A. MATLAB: An Introduction with Applications 2nd Edition. – John Wiley & Sons. ISBN 978-0-471-69420-5.– 2004.
6. MATLAB technical documentation [Access] http://www.mathworks.com/access/helpdesk/help/toolbox/bioinfo/ref/seqtool.html
7. http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML
8. Водолазкий В,Семериков В. Энциклопедия PERL. СПб.: Питер. - 2002.-576С.
9. ftp://ftp.ncbi.nih.gov/genbank/genomes/H_sapiens
10. International Human Genome Sequencing Consortium. The NCBI Handbook [Web resource]: Bethesda National Library of Medicine (US), NCBI 2002-2005 / edit. J. McEntyre, J. Ostell . – [Access]: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook
11. The DDBJ/EMBL/GenBank Feature Table: Definition [Web resource]: Bethesda.– 2007 / International Sequence Databank Collaboration.– [Access]: http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html#7.4
12. NCBI Help Manual.– Bethesda (MD): National Library of Medicine (US), NCBI; 2005-2009.
13. Компиляторы: принципы, технологии и инструментарий / А. В. Ахо, М. С. Лам, Р. Сети, Д. Д. Ульман. – М.: Вильямс. –2008. –2-е издание. –1184 c.
14. Wain H. M., Bruford E. A., Lovering R. C., Lush M. J., Wright M. W. and Povey S. Guidelines for Human Gene Nomenclature//Genomics.-2002.-№79(4). - Р. 464-470.
15. Пат. 43786 Україна, МПК (2007) G 06 F, 17/21. Спосіб перетворення структури послідовностей генів бази даних / Дуплій Д.Р., Калашніков В.В., Чащин Н.А., заявник та патентовласник Київ. Ін-т Молекулярної Біології и Генетики; Держ.реєстр. від 25.08.09.
Cited
How to Cite
Duplij, D. R., Kalashnikov, V. V., & Chashyn, N. A. (1). How to obtain the nucleotide sequences DNA from gene bank data base. Biophysical Bulletin, 1(24). Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/4026
Section
Methods of biophysical investigations
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