Types and frequencies of sequencing errors in methyl-filtered and high C0t maize genome survey sequences

Plant Physiology

Volumn 135, Issue 4, 2004, Pages 2040-2045

  Fu, Yan ^a   Hsia, An Ping ^a   Guo, Ling ^a   Schnable, Patrick S ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ERROR ANALYSIS; FILTRATION; GENETIC ENGINEERING;

GENOMES; POLYMORPHISMS; VECTOR TRIMMINGS;

PLANTS (BOTANY);

ERRORS; FILTRATION; GENETIC ENGINEERING; PLANTS;

EMBRYOPHYTA; ZEA; ZEA MAYS;

EID: 4444264887     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.041640     Document Type: Review

References (12)

1. Bailey J, Gu Z, Clark R, Reinert K, Samonte R, Schwartz S, Adams M, Myers E, Li P, Eichler E (2002) Recent segmental duplications in the human genome. Science 297: 1003-1007
2. Bailey J, Yavor A, Massa H, Trask B, Eichler E (2001) Segmental duplications: organization and impact within the current human genome project assembly. Genome Res 11: 1005-1017
3. Brown KR, Weatherdon KL, Galligan CL, Skalski V (2002) A nuclear 3′-5′ exonuclease proofreads for the exonuclease-deficient DNA polymerase alpha. DNA Repair (Amst) 1: 795-810
4. Chou HH, Holmes MH (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104
5. Emrich SJ, Aluru S, Fu Y, Wen TJ, Narayanan M, Guo L, Ashlock D, Schnable PS (2004) A strategy for assembling the maize (Zea mays L.) genome. Bioinformatics 20: 140-147
6. Hurles M (2002) Are 100,000 "SNPs" useless? Science 298: 1509
7. Kunkel TA, Bebenek K (2000) DNA replication fidelity. Annu Rev Biochem 69: 497-529
8. Palmer LE, Rabinowicz PD, O'Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR (2003) Maize genome sequencing by methylation filtration. Science 302: 2115-2117
9. Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Parnell LD, Stein L, McCombie WR, Martienssen RA (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat Genet 23: 305-308
10. Schaaper RM (1993) Base selection, proofreading and mismatch repair during DNA replication in Escherichia coli. J Biol Chem 268: 23762-23765
11. Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, et al (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120
12. ot sequence analysis of the maize genome. Plant J 49: 249-255