Literature DB >> 17018534

GenoProfiler: batch processing of high-throughput capillary fingerprinting data.

Frank M You1, Ming-Cheng Luo, Yong Qiang Gu, Gerard R Lazo, Karin Deal, Jan Dvorak, Olin D Anderson.   

Abstract

UNLABELLED: High-throughput content fingerprinting techniques employing capillary electrophoresis place new demands on the editing of fingerprint files for the downstream contig assembly program, FPC. A cross-platform software application, GenoProfiler, was developed for automated editing of sized fingerprinting profiles generated by the ABI Genetic Analyzers. The batch-processing module extracts the sized fragment information directly from the ABI raw trace files, or from data files exported from GeneMapper or other size calling software, removes the background noise and undesired fragments, and generates fragment size files compatible with the FPC software. AVAILABILITY: http://wheat.pw.usda.gov/PhysicalMapping/

Entities:  

Mesh：

Year:  2006        PMID： 17018534     DOI： 10.1093/bioinformatics/btl494

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  23 in total

1.  Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict.

Authors:  Cheng Deng; C-H Christina Cheng; Hua Ye; Ximiao He; Liangbiao Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-29       Impact factor: 11.205

2.  Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar.

Authors:  Simone Scalabrin; Michela Troggio; Marco Moroldo; Massimo Pindo; Nicoletta Felice; Giuseppina Coppola; Giacomo Prete; Giulia Malacarne; Raffaella Marconi; Giorgia Faes; Irena Jurman; Stella Grando; Taco Jesse; Cinzia Segala; Giorgio Valle; Alberto Policriti; Paolo Fontana; Michele Morgante; Riccardo Velasco
Journal:  BMC Genomics       Date:  2010-03-26       Impact factor: 3.969

3.  CD4+CD25+Foxp3+ regulatory T cells optimize diversity of the conventional T cell repertoire during reconstitution from lymphopenia.

Authors:  Colleen J Winstead; Cavan S Reilly; James J Moon; Marc K Jenkins; Sara E Hamilton; Stephen C Jameson; Sing Sing Way; Alexander Khoruts
Journal:  J Immunol       Date:  2010-03-31       Impact factor: 5.422

4.  A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome.

Authors:  Francis Parlange; Simone Oberhaensli; James Breen; Matthias Platzer; Stefan Taudien; Hana Simková; Thomas Wicker; Jaroslav Doležel; Beat Keller
Journal:  Funct Integr Genomics       Date:  2011-08-02       Impact factor: 3.410

5.  Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species.

Authors:  Ming-Cheng Luo; Yaqin Ma; Frank M You; Olin D Anderson; David Kopecký; Hana Simková; Jan Safár; Jaroslav Dolezel; Bikram Gill; Patrick E McGuire; Jan Dvorak
Journal:  BMC Genomics       Date:  2010-02-19       Impact factor: 3.969

6.  A first generation BAC-based physical map of the Asian seabass (Lates calcarifer).

Authors:  Jun Hong Xia; Felicia Feng; Grace Lin; Chun Ming Wang; Gen Hua Yue
Journal:  PLoS One       Date:  2010-08-05       Impact factor: 3.240

7.  A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat.

Authors:  Yong Q Gu; Yaqin Ma; Naxin Huo; John P Vogel; Frank M You; Gerard R Lazo; William M Nelson; Carol Soderlund; Jan Dvorak; Olin D Anderson; Ming-Cheng Luo
Journal:  BMC Genomics       Date:  2009-10-27       Impact factor: 3.969

8.  A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.

Authors:  Ming-Cheng Luo; Yong Q Gu; Frank M You; Karin R Deal; Yaqin Ma; Yuqin Hu; Naxin Huo; Yi Wang; Jirui Wang; Shiyong Chen; Chad M Jorgensen; Yong Zhang; Patrick E McGuire; Shiran Pasternak; Joshua C Stein; Doreen Ware; Melissa Kramer; W Richard McCombie; Shahryar F Kianian; Mihaela M Martis; Klaus F X Mayer; Sunish K Sehgal; Wanlong Li; Bikram S Gill; Michael W Bevan; Hana Simková; Jaroslav Dolezel; Song Weining; Gerard R Lazo; Olin D Anderson; Jan Dvorak
Journal:  Proc Natl Acad Sci U S A       Date:  2013-04-22       Impact factor: 11.205

9.  Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A.

Authors:  Stuart J Lucas; Bala Anı Akpınar; Melda Kantar; Zohar Weinstein; Fatma Aydınoğlu; Jan Safář; Hana Simková; Zeev Frenkel; Abraham Korol; Federica Magni; Federica Cattonaro; Sonia Vautrin; Arnaud Bellec; Hélène Bergès; Jaroslav Doležel; Hikmet Budak
Journal:  PLoS One       Date:  2013-04-16       Impact factor: 3.240

10.  Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea.

Authors:  Zahra-Katy Navabi; Terry Huebert; Andrew G Sharpe; Carmel M O'Neill; Ian Bancroft; Isobel A P Parkin
Journal:  BMC Genomics       Date:  2013-04-15       Impact factor: 3.969
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