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Items: 1 to 20 of 76

1.

Expedited batch processing and analysis of transposon insertions.

Smith JD, Ray DA.

BMC Res Notes. 2011 Nov 4;4:482. doi: 10.1186/1756-0500-4-482.

2.

Transposable element annotation of the rice genome.

Juretic N, Bureau TE, Bruskiewich RM.

Bioinformatics. 2004 Jan 22;20(2):155-60.

PMID:
14734305
3.

BRM-Parser: a tool for comprehensive analysis of BLAST and RepeatMasker results.

Bajpai A, Sridhar S, Reddy HM, Jesudasan RA.

In Silico Biol. 2007;7(4-5):399-403.

PMID:
18391232
4.

TAPDANCE: an automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data.

Sarver AL, Erdman J, Starr T, Largaespada DA, Silverstein KA.

BMC Bioinformatics. 2012 Jun 29;13:154. doi: 10.1186/1471-2105-13-154.

5.

ModuleOrganizer: detecting modules in families of transposable elements.

Tempel S, Rousseau C, Tahi F, Nicolas J.

BMC Bioinformatics. 2010 Sep 22;11:474. doi: 10.1186/1471-2105-11-474.

6.

Analysis of transposable element sequences using CENSOR and RepeatMasker.

Huda A, Jordan IK.

Methods Mol Biol. 2009;537:323-36. doi: 10.1007/978-1-59745-251-9_16.

PMID:
19378152
7.

Identification of piggyBac-mediated insertions in Plasmodium berghei by next generation sequencing.

Cao Y, Rui B, Wellems DL, Li M, Chen B, Zhang D, Pan W.

Malar J. 2013 Aug 21;12:287. doi: 10.1186/1475-2875-12-287.

8.

P Transposable Elements in Drosophila and other Eukaryotic Organisms.

Majumdar S, Rio DC.

Microbiol Spectr. 2015 Apr;3(2):MDNA3-0004-2014. doi: 10.1128/microbiolspec.MDNA3-0004-2014. Review.

PMID:
26104714
9.

Batch Blast Extractor: an automated blastx parser application.

Pirooznia M, Perkins EJ, Deng Y.

BMC Genomics. 2008 Sep 16;9 Suppl 2:S10. doi: 10.1186/1471-2164-9-S2-S10.

10.

TaxMan: a taxonomic database manager.

Jones M, Blaxter M.

BMC Bioinformatics. 2006 Dec 18;7:536.

11.

T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data.

Fiston-Lavier AS, Carrigan M, Petrov DA, González J.

Nucleic Acids Res. 2011 Mar;39(6):e36. doi: 10.1093/nar/gkq1291. Epub 2010 Dec 21.

12.

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

Barrick JE, Colburn G, Deatherage DE, Traverse CC, Strand MD, Borges JJ, Knoester DB, Reba A, Meyer AG.

BMC Genomics. 2014 Nov 29;15:1039. doi: 10.1186/1471-2164-15-1039.

13.
14.

A P-element insertion screen identified mutations in 455 novel essential genes in Drosophila.

Oh SW, Kingsley T, Shin HH, Zheng Z, Chen HW, Chen X, Wang H, Ruan P, Moody M, Hou SX.

Genetics. 2003 Jan;163(1):195-201.

15.

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression.

Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T, Wessler SR.

Nature. 2009 Oct 22;461(7267):1130-4. doi: 10.1038/nature08479.

PMID:
19847266
16.

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, Wei CL, Sung WK, Ruan Y.

BMC Bioinformatics. 2006 Aug 25;7:390.

17.

Identification of a high frequency transposon induced by tissue culture, nDaiZ, a member of the hAT family in rice.

Huang J, Zhang K, Shen Y, Huang Z, Li M, Tang D, Gu M, Cheng Z.

Genomics. 2009 Mar;93(3):274-81. doi: 10.1016/j.ygeno.2008.11.007. Epub 2008 Dec 23.

18.

New transposable elements identified as insertions in rice transposon Tnr1.

Han CG, Frank MJ, Ohtsubo H, Ohtsubo E.

Genes Genet Syst. 2000 Apr;75(2):69-77.

19.

The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes.

Estill JC, Bennetzen JL.

Plant Methods. 2009 Jun 19;5:8. doi: 10.1186/1746-4811-5-8.

20.

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