Greene SCPrimer: A rapid comprehensive tool for designing degenerate primers from multiple sequence alignments

Nucleic Acids Research

Volumn 34, Issue 22, 2006, Pages 6605-6611

  Jabado, Omar J ^a   Palacios, Gustavo ^a   Kapoor, Vishal ^a   Hui, Jeffrey ^a   Renwick, Neil ^a   Zhai, Junhui ^a   Briese, Thomas ^a   Lipkin, W Ian ^a  

^a Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER RNA;

ALGORITHM; ARTICLE; BASE MISPAIRING; BASE PAIRING; COMPUTER PROGRAM; EBOLA VIRUS; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RIFT VALLEY FEVER BUNYAVIRUS; RNA SEQUENCE; SEOUL VIRUS; SEQUENCE ALIGNMENT; VIRUS GENE; VIRUS HEMORRHAGIC FEVER; VIRUS INFECTION; VIRUS VIRULENCE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA PRIMERS; DNA, VIRAL; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 33845898161     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl966     Document Type: Article

References (42)

1. Bustin,S.A. (2002) Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): Trends and problems. J. Mol. Endocrinol., 29, 23-39.
2. Rose,T.M., Henikoff,J.G. and Henikoff,S. (2003) CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res., 31, 3763-3766.
3. Ehlers,B., Borchers,K., Grund,C., Frolich,K., Ludwig,H. and Buhk,H.J. (1999) Detection of new DNA polymerase genes of known and potentially novel herpesviruses by PCR with degenerate and deoxyinosine-substituted primers. Virus Genes, 18, 211-220.
4. Chen,Z. and Plagemann,P.G. (1995) Detection of related positive-strand RNA virus genomes by reverse transcription/polymerase chain reaction using degenerate primers for common replicase sequences. Virus Res., 39, 365-375.
5. Briese,T., Jia,X.Y., Huang,C., Grady,L.J. and Lipkin,W.I. (1999) Identification of a Kunjin/West Nile-like flavivirus in brains of patients with New York encephalitis. Lancet, 354, 1261-1262.
6. Briese,T., Rambaut,A. and Lipkin,W.I. (2004) Analysis of the medium (M) segment sequence of Guaroa virus and its comparison to other orthobunyaviruses. J. Gen. Virol., 85, 3071-3077.
7. Buck,G.A., Fox,J.W., Gunthorpe,M., Hager,K.M., Naeve,C.W., Pon,R.T., Adams,P.S. and Rush,J. (1999) Design strategies and performance of custom DNA sequencing primers. Biotechniques, 27, 528-536.
8. Piotr Rychlik,W.R. (2005) Oligo Software for Primer Design. Molecular Biology Insights, Inc.
9. Rozen,S. and Skaletsky,H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.
10. Kampke,T., Kieninger,M. and Mecklenburg,M. (2001) Efficient primer design algorithms. Bioinformatics, 17, 214-225.
11. Xu,D., Li,G., Wu,L., Zhou,J. and Xu,Y. (2002) PRIMEGENS: Robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics, 18, 1432-1437.
12. Emrich,S.J., Lowe,M. and Delcher,A.L. (2003) PROBEmer: A web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res., 31, 3746-3750.
13. Linhart,C. and Shamir,R. (2002) The degenerate primer design problem. Bioinformatics, 18, S172-181.
14. Doi,K. and Imai,H. (1999) A greedy algorithm for minimizing the number of primers in multiple PCR experiments. Genome Inform. Ser Workshop Genome Inform., 10, 73-82.
15. Giegerich,R., Meyer,F. and Schleiermacher,C. (1996) GeneFisher - software support for the detection of postulated genes. Proc. Int. Conf. Intell. Syst. Mol. Biol., 4, 68-77.
16. Souvenir,R., Buhler,J., Stormo,G. and Zhang,W. (2003) In Gary Benson,R.P. (ed.), Algorithms in Bioinformatics: Third International Workshop, WABI 2003. Springer Berlin/Heidelberg, Budapest, Hungary, Vol. 2812, pp. 512-526.
17. Jarman,S.N. (2004) Amplicon: Software for designing PCR primers on aligned DNA sequences. Bioinformatics, 20, 1644-1645.
18. Huang,Y.C., Chang,C.F., Chan,C.H., Yeh,T.J., Chang,Y.C., Chen,C.C. and Kao,C.Y. (2005) Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens. Bioinformatics, 21, 4330-4337.
19. Rachlin,J., Ding,C., Cantor,C. and Kasif,S. (2005) MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Res., 33, W544-W547.
20. Garey,M.R. and Johnson,D.S. (1979) Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman, New York.
21. Aickelin,U. (2002) An indirect genetic algorithm for set covering problems. J. Oper. Res. Soc., 53, 1118-1126.
22. Sen,S. (1993) In Ed Deaton,K.G., Hal,Berghel and George,Hedrick (eds), Proceedings of the 1993 ACM/SIGAPP symposium on Applied computing: States of the Art and Practice. New York, NY, 14-16 February 1993. Indianapolis, Indian, USA, pp. 157-164.
23. Caprara,A., Fischetti,M. and Toth,P. (1999) A heuristic method for the set covering problem. Oper. Res., 47, 730-743.
24. Slavik,P. (1997) A tight analysis of the greedy algorithm for set cover. J. Algorithms, 25, 237-254.
25. Caprara,A., Toth,P. and Fischetti,M. (2000) Algorithms for the set covering problem. Ann. Oper. Res., 98, 353-371.
26. Woodbury,M.A., Ciftan,E.A. and Amos,D.B. (1979) HLA serum screening based on an heuristic solution of the set cover problem. Comput. Programs Biomed., 9, 263-273.
27. Zhao,W., Fanning,M.L. and Lane,T. (2005) Efficient RNAi-based gene family knockdown via set cover optimization. Artif. Intell. Med., 35, 61-73.
28. Doi,K. and Imai,H. (1997) Greedy algorithms for finding a small set of primers satisfying cover and length resolution conditions in PCR experiments. Genome Inform. Ser Workshop Genome Inform., 8, 43-52.
29. DasGupta,B., Konwar,K.M., Mandoiu,I.I. and Shvartsman,A.A. (2005) Highly scalable algorithms for robust string barcoding. Int. J. Bioinform. Res. Appl., 1, 145-161.
30. de Hoon,M.J., Imoto,S., Nolan,J. and Miyano,S. (2004) Open source clustering software. Bioinformatics, 20, 1453-1454.
31. Le Novere,N. (2001) MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics, 17, 1226-1227.
32. Rychlik,W. and Rhoads,R.E. (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res., 17, 8543-8551.
33. Macken,C., Lu,H., Goodman,J. and Boykin,L. (2001) The value of a database in surveillance and vaccine selection. In Options for the Control of Influenza IV: Proceedings of the World Congress on Options for the Control of Influenza IV, Crete, Greece, 23-28 September 2000. Elsevier, Amsterdam; New York, pp. 103-106.
34. Chenna,R., Sugawara,H., Koike,T., Lopez,R., Gibson,T.J., Higgins,D.G. and Thompson,J.D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500.
35. Day,W.H.E. and Edelsbrunner,H. (1984) Efficient algorithms for agglomerative hierarchical-clustering methods. J. Classif., 1, 7-24.
36. Papadimitriou,C.H. (1995) Computational Complexity. Addison-Wesley, Reading, Mass.
37. Peters,W. (2002) Novel and challenging infections of man. A brief overview. Parassitologia, 44, 33-42.
38. Geisbert,T.W. and Jahrling,P.B. (2004) Exotic emerging viral diseases: progress and challenges. Nature Med., 10, S110-121.
39. Drosten,C., Kummerer,B.M., Schmitz,H. and Gunther,S. (2003) Molecular diagnostics of viral hemorrhagic fevers. Antiviral Res., 57, 61-87.
40. Palacios,G., Briese,T., Kapoor,V., Jabado,O., Liu,Z., Venter,M., Zhai,J., Renwick,N., Grolla,A., Geisbert,T.W. et al. (2006) MassTag polymerase chain reaction for differential diagnosis of viral hemorrhagic fevers. Emerging Infect. Dis., 12, 692-695.
41. Briese,T., Palacios,G., Kokoris,M., Jabado,O., Liu,Z., Renwick,N., Kapoor,V., Casas,I., Pozo,F., Limberger,R. et al. (2005) Diagnostic system for rapid and sensitive differential detection of pathogens. Emerging Infect. Dis., 11, 310-313.
42. Rose,T.M. (2005) CODEHOP-mediated PCR - a powerful technique for the identification and characterization of viral genomes. Virol. J., 2, 20.