Skip Navigation

This Article
Right arrow Print PDF (412K)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (108)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Dumas, J.-P.
Right arrow Articles by Ninio, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Dumas, J.-P.
Right arrow Articles by Ninio, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 1982, Vol. 10, No. 1 197-206
© 1982

Articles

Efficient algorithms for folding and comparing nucleic acid sequences

Jean-Pierre Dumas and Jacques Ninio

Biochimie de l'évolution, I.R.B.M. Tour 43, 2 Place Jussieu, 75251 Paris Cedex 05, France

Received September 3, 1981. Fast algorithms for analysing sequence data are presented. An algorithm for strict homologies finds all common subsequences of length ≥ 6 in two given sequences. With it, nucleic acid pieces five thousand nucleotides long can be compared in five seconds on CDC 6600. Secondary structure algorithms generate the N most stable secondary structures of an RNA molecule, taking into account all loop contributions, and the formation of all possible base-pairs in stems, including odd pairs (G.G., C.U., etc.). They allow a typical 100-nucleotide sequence to be analysed in 10 seconds. The homology and secondary structure programs are respectively illustrated with a comparison of two phage genomes, and a discussion of Drosophila melanogaster 5S RNA folding.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
O. Gotoh
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence
Nucleic Acids Res., May 1, 2008; 36(8): 2630 - 2638.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
X. Huang, S.-P. Yang, A. T. Chinwalla, L. W. Hillier, P. Minx, E. R. Mardis, and R. K. Wilson
Application of a superword array in genome assembly
Nucleic Acids Res., January 5, 2006; 34(1): 201 - 205.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
M Zuker
On finding all suboptimal foldings of an RNA molecule
Science, April 7, 1989; 244(4900): 48 - 52.
[Abstract] [PDF]

Home page
 Genes Dev.Home page
T Toda, S Cameron, P Sass, and M Wigler
SCH9, a gene of Saccharomyces cerevisiae that encodes a protein distinct from, but functionally and structurally related to, cAMP-dependent protein kinase catalytic subunits.
Genes & Dev., May 1, 1988; 2(5): 517 - 527.
[Abstract] [PDF]

Home page
 ScienceHome page
D. Lipman and W. Pearson
Rapid and sensitive protein similarity searches
Science, March 22, 1985; 227(4693): 1435 - 1441.
[Abstract] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.