InsertionMapper: A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Xiong, Wenwei ^a   He, Limei ^b   Li, Yubin ^b   Dooner, Hugo K ^b   Du, Chunguang ^a  

^a MONTCLAIR STATE UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

Multidimensional pooling; Next generation sequencing; Sequence identification; Target enrichment

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DATA BASE; DATA PROCESSING; EXON; GENE AMPLIFICATION; GENE IDENTIFICATION; GENE INSERTION; GENE MAPPING; GENE SEQUENCE; GENE TARGETING; HIGH THROUGHPUT SEQUENCING; MAIZE; NEXT GENERATION SEQUENCING; NONHUMAN; PLANT GENETICS; PLANT GENOME; POLYMERASE CHAIN REACTION; REVERSE GENETICS; SEQUENCE ALIGNMENT; TRANSPOSON; BIOLOGY; GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; REPRODUCIBILITY;

ZEA MAYS;

TRANSPOSON;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA TRANSPOSABLE ELEMENTS; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SOFTWARE; ZEA MAYS;

EID: 84884967275     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-679     Document Type: Article

References (16)

1. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26(10):1135-1145. 10.1038/nbt1486, 18846087.
2. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31-46. 10.1038/nrg2626, 19997069.
3. Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008, 24(3):133-141. 10.1016/j.tig.2007.12.007, 18262675.
4. Zwaal RR, Broeks A, van Meurs J, Groenen JT, Plasterk RH. Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank. Proc Natl Acad Sci U S A 1993, 90(16):7431-7435. 10.1073/pnas.90.16.7431, 47155, 8395047.
5. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Target-enrichment strategies for next-generation sequencing. Nat Methods 2010, 7(2):111-118. 10.1038/nmeth.1419, 20111037.
6. Nijman IJ, Mokry M, van Boxtel R, Toonen P, de Bruijn E, Cuppen E. Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples. Nat Methods 2010, 7(11):913-915. 10.1038/nmeth.1516, 20953175.
7. Vandenbussche M, Janssen A, Zethof J, van Orsouw N, Peters J, van Eijk MJ, Rijpkema AS, Schneiders H, Santhanam P, de Been M, et al. Generation of a 3D indexed Petunia insertion database for reverse genetics. Plant J 2008, 54(6):1105-1114. 10.1111/j.1365-313X.2008.03482.x, 18346192.
8. Marroni F, Pinosio S, Morgante M. The quest for rare variants: pooled multiplexed next generation sequencing in plants. Front Plant Sci 2012, 3:133. 3384946, 22754557.
9. Du C, Hoffman A, He L, Caronna J, Dooner HK. The complete Ac/Ds transposon family of maize. BMC Genomics 2011, 12:588. 10.1186/1471-2164-12-588, 3260210, 22132901.
10. Fu H, Dooner HK. Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci U S A 2002, 99(14):9573-9578. 10.1073/pnas.132259199, 123182, 12060715.
11. McClintock B. Chromosome organization and genic expression. Cold Spring Harb Symp Quant Biol 1951, 16:13-47. 10.1101/SQB.1951.016.01.004, 14942727.
12. Cowperthwaite M, Park W, Xu Z, Yan X, Maurais SC, Dooner HK. Use of the transposon Ac as a gene-searching engine in the maize genome. Plant Cell 2002, 14(3):713-726. 10.1105/tpc.010468, 150591, 11910016.
13. Vollbrecht E, Duvick J, Schares JP, Ahern KR, Deewatthanawong P, Xu L, Conrad LJ, Kikuchi K, Kubinec TA, Hall BD, et al. Genome-wide distribution of transposed Dissociation elements in maize. Plant Cell 2010, 22(6):1667-1685. 10.1105/tpc.109.073452, 2910982, 20581308.
14. Frame BR, Shou H, Chikwamba RK, Zhang Z, Xiang C, Fonger TM, Pegg SE, Li B, Nettleton DS, Pei D, et al. Agrobacterium tumefaciens-mediated transformation of maize embryos using a standard binary vector system. Plant Physiol 2002, 129(1):13-22. 10.1104/pp.000653, 1540222, 12011333.
15. Li Y, Segal G, Wang Q, Dooner HK. Gene tagging with engineered ds elements in maize. Methods Mol Biol 2013, 1057:83-99. 10.1007/978-1-62703-568-2_6, 23918422.
16. Schaeffer ML, Harper LC, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Sen TZ, Lawrence CJ. MaizeGDB: curation and outreach go hand-in-hand. Database (Oxford) 2011, 2011:bar022.