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. 1984 Jan 11;12(1 Pt 1):193–201. doi: 10.1093/nar/12.1part1.193

Simplified computer programs for search of homology within nucleotide sequences.

M Kröger, A Kröger-Block
PMCID: PMC320996  PMID: 6546417

Abstract

Four new computer programs for search of homology within nucleotide sequences are presented. The main scope of the program design is flexibility, independence of sequence length and the capability to be used by any molecular biologist without any prior computer experience. The programs offer a linear search, a search for maximal identity, an alignment along a given sequence and a search based on homology within the amino acid coding capacity of nucleotide sequences. The language is Fortran V. Copies are available on request.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Dumas J. P., Ninio J. Efficient algorithms for folding and comparing nucleic acid sequences. Nucleic Acids Res. 1982 Jan 11;10(1):197–206. doi: 10.1093/nar/10.1.197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Felsenstein J., Sawyer S., Kochin R. An efficient method for matching nucleic acid sequences. Nucleic Acids Res. 1982 Jan 11;10(1):133–139. doi: 10.1093/nar/10.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Goad W. B., Kanehisa M. I. Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries. Nucleic Acids Res. 1982 Jan 11;10(1):247–263. doi: 10.1093/nar/10.1.247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Harr R., Hagblom P., Gustafsson P. Two-dimensional graphic analysis of DNA sequence homologies. Nucleic Acids Res. 1982 Jan 11;10(1):365–374. doi: 10.1093/nar/10.1.365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Kröger M., Kröger-Block A. A flexible new computer program for handling DNA sequence data. Nucleic Acids Res. 1982 Jan 11;10(1):229–236. doi: 10.1093/nar/10.1.229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Novotny J. Matrix program to analyze primary structure homology. Nucleic Acids Res. 1982 Jan 11;10(1):127–131. doi: 10.1093/nar/10.1.127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Queen C., Wegman M. N., Korn L. J. Improvements to a program for DNA analysis: a procedure to find homologies among many sequences. Nucleic Acids Res. 1982 Jan 11;10(1):449–456. doi: 10.1093/nar/10.1.449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Sankoff D., Cedergren R. J., McKay W. A strategy for sequence phylogeny research. Nucleic Acids Res. 1982 Jan 11;10(1):421–431. doi: 10.1093/nar/10.1.421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Staden R. Sequence data handling by computer. Nucleic Acids Res. 1977 Nov;4(11):4037–4051. doi: 10.1093/nar/4.11.4037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Stockwell P. A. A large database DNA sequence handling program with generalized searching specifications. Nucleic Acids Res. 1982 Jan 11;10(1):115–125. doi: 10.1093/nar/10.1.115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Wilbur W. J., Lipman D. J. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983 Feb;80(3):726–730. doi: 10.1073/pnas.80.3.726. [DOI] [PMC free article] [PubMed] [Google Scholar]

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