Method and apparatus for determining consensus secondary structu

Details Method and apparatus for determining consensus secondary structu Method and apparatus for determining consensus secondary structu

1995-06-06

1998-12-01

Degen, Nancy

Chemistry: analytical and immunological testing

Heterocyclic carbon compound

Hetero-o

G01N 3300

Patent

active

058437320

ABSTRACT:
An interactive computer program generates a composite dot matrix representation of secondary structure elements from a set of functionally related oligonucleotides. The composite image facilitates visual detection of conserved secondary structure motifs with similar sequence sets. The complete pattern displaying all possible base pairings can be readily pruned with two progressive filters to provide the user with a simplified figure displaying only the most stable and conserved regions. Additional simplification of the structure matrix image can be achieved by eliminating mutually exclusive structures. Alignment editing provided within the program facilitates refinement of the consensus secondary structure.

REFERENCES:
patent: 5270163 (1993-12-01), Gold et al.
Le et al., "A method for predicting common structures of homologous RNAs", Computers Biomed. Res., 28: 53-66, May 1995.
Chan et al., "A computer method for finding common base paired helices in aligned sequences: application to the analysis of random sequences", Nucleic Acids Res., 19(2): 353-358, 1991.
De Rijk et al., "DCSE, an interactive tool for sequence alignment and secondary structure research", Computer Appl. Biosci., 9(6): 735-740, 1993.
Waterman, M.S. (1988) Consensus Methods for Folding Single-Stranded Nucleic Acids, in Waterman, M.S. ed., Mathematical Methods for DNA Sequences, CRC Press, Boca Raton, Florida, Chapter 8, pp. 185-223.
Bartel and Szostak (1993) Science 261:1141-1148.
Beaudry and Joyce (1992) Science 257:635-641.
Bock et al. (1992) Nature 355:564-566.
Ellington and Szostak (1990) Nature 346:818-822.
Feng and Doolittle (1987) J. Mol. Evol. 25:351-360.
Gold et al. (1993) in The RNA World, eds., Gespeland and Atkins, Cold Spring Harbor Laboratory Press, Plainview NY, Chapter 19, 497-509.
Gutell et al. (1992) Nucleic Acids Res. 20:5785-5795.
Han and Kim (1993) Nucleic Acids Res. 21:1251-1257.
Illangasekare et al. (1995) Science 267:243-247.
Jaeger et al. (1990) Methods in Enzymology 183:281-306.
Jaeger et al. (1989) Proc. Natl. Acad. Sci. USA 86:7706-7710.
Jellinek et al. (1993) Proc. Natl. Acad. Sci. USA 90:11227-11231.
Jellinek et al. (1994) Biochemistry 33:10450-10456.
Jenison et al. (1994) Science 263:1425-1428.
Kubik et al. (1994) Nucleic Acids Res. 22:2619-2626.
Lin et al. (1994) Nucleic Acids Res. 22:5229-5234.
Pan and Uhlenbeck (1992) Nature 358:560-563.
Quigley et al. (1984) Nucleic Acids Res. 12:347-366.
Steinberg et al. (1993) Nucleic Acids Res. 21:3011-3015.
Tuerk et al. (1992) Proc. Natl. Acad. Sci. USA 89:6988-6992.
Tuerk and Gold (1990) Science 249:505-510.
Woese and Pace (1993) in The RNA World, eds., Gespeland and Atkins, Cold Spring Harbor Laboratory Press, Plainview, NY. Chapter 4, 91-117.
Zuker (1989) Science 244:48.

Affiliated with

Also associated with

Rating

Method and apparatus for determining consensus secondary structu does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Method and apparatus for determining consensus secondary structu, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method and apparatus for determining consensus secondary structu will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-2395015