CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3763-3766

  Rose, Timothy M ^b   Henikoff, Jorja G ^a   Henikoff, Steven ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PRIMER DNA; OLIGONUCLEOTIDE;

AMINO ACID SEQUENCE; ANIMAL GENETICS; ARTICLE; BACTERIAL GENETICS; CODON; COMPUTER PROGRAM; CONTROLLED STUDY; GENE AMPLIFICATION; GENE ISOLATION; GENETIC CONSERVATION; INTERNET; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PARALOGY; PLANT GENETICS; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; CHEMISTRY; COMPUTER INTERFACE; CONSENSUS SEQUENCE; METHODOLOGY;

ANIMALIA; BACTERIA (MICROORGANISMS);

AMINO ACID SEQUENCE; BASE SEQUENCE; CONSENSUS SEQUENCE; DNA PRIMERS; INTERNET; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 0043122986     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg524     Document Type: Article

References (9)

1. Rose,T.M., Schultz,E.R., Henikoff,J.G., Pietrokovski,S., McCallum,C.M. and Henikoff,S. (1998) Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res., 26, 1628-1635.
2. Henikoff,J.G., Pietrokovski,S., McCallum,C.M. and Henikoff,S. (2000) Blocks-based methods for detecting protein homology. Electrophoresis, 21, 1700-1706.
3. Henikoff,J.G. and Henikoff,S. (1996) Using substitution probabilities to improve position-specific scoring matrices. Comput. Appl. Biosci., 12, 135-143.
4. Rychlik,W., Spencer,W.J. and Rhoads,R.E. (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res., 18, 6409-6412.
5. Henikoff,S. and Henikoff,J.G. (1994) Position-based sequence weights. J. Mol. Biol., 243, 574-578.
6. Morant,M., Hehn,A. and Werck-Reichhart,D. (2002) Conservation and diversity of gene families explored using the CODEHOP strategy in higher plants. BMC Plant Biol., 2, 7.
7. Schultz,E.R., Rankin,G.W Jr., Blanc,M.P., Raden,B.W., Tsai,C.C. and Rose,T.M. (2000) Characterization of two divergent lineages of macaque rhadinovituses related to Kaposi's sarcoma-associated herpesvirus. J. Virol., 74, 4919-4928.
8. Rose,T.M., Ryan,J.T, Schultz,E.R., Raden,B.W., Tsai,C.-C. (2003) Analysis of 4.3 Kb of the divergent locus-B of macaque retroperitoneal fibromatosis-associated herpesvirus (RFHV) reveals close similarity to Kaposi's sarcoma-associated herpesvirus (KSHV) in gene sequence and genome organization. J. Virol., in press.
9. Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.