Literature DB >> 11934749

Assembly of fingerprint contigs: parallelized FPC.

S R Ness1, W Terpstra, M Krzywinski, M A Marra, S J M Jones.   

Abstract

SUMMARY: One of the more common uses of the program FingerPrint Contigs (FPC) is to assemble random restriction digest 'fingerprints' of overlapping genomic clones into contigs. To improve the rate of assembling contigs from large fingerprint databases we have adapted FPC so that it can be run in parallel on multiple processors and servers. The current version of 'parallelized FPC' has been used in our laboratory to assemble mammalian BAC fingerprint databases, each containing more than 300000 BAC fingerprints. AVAILABILITY: This parallelized version of FPC is available under the GNU GPL licence, and can be downloaded from ftp://ftp.bcgsc.bc.ca/pub/fpcd.

Entities:  

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Year:  2002        PMID： 11934749     DOI： 10.1093/bioinformatics/18.3.484

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


  6 in total

1.  Physical map-assisted whole-genome shotgun sequence assemblies.

Authors:  René L Warren; Dmitry Varabei; Darren Platt; Xiaoqiu Huang; David Messina; Shiaw-Pyng Yang; James W Kronstad; Martin Krzywinski; Wesley C Warren; John W Wallis; LaDeana W Hillier; Asif T Chinwalla; Jacqueline E Schein; Asim S Siddiqui; Marco A Marra; Richard K Wilson; Steven J M Jones
Journal:  Genome Res       Date:  2006-06       Impact factor: 9.043

2.  Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.

Authors:  René Warren; William W L Hsiao; Hisashi Kudo; Matt Myhre; Manisha Dosanjh; Anca Petrescu; Hiroyuki Kobayashi; Satoru Shimizu; Keisuke Miyauchi; Eiji Masai; George Yang; Jeff M Stott; Jacquie E Schein; Heesun Shin; Jaswinder Khattra; Duane Smailus; Yaron S Butterfield; Asim Siddiqui; Robert Holt; Marco A Marra; Steven J M Jones; William W Mohn; Fiona S L Brinkman; Masao Fukuda; Julian Davies; Lindsay D Eltis
Journal:  J Bacteriol       Date:  2004-11       Impact factor: 3.490

3.  Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome.

Authors:  Martin Krzywinski; John Wallis; Claudia Gösele; Ian Bosdet; Readman Chiu; Tina Graves; Oliver Hummel; Dan Layman; Carrie Mathewson; Natasja Wye; Baoli Zhu; Derek Albracht; Jennifer Asano; Sarah Barber; Mabel Brown-John; Susanna Chan; Steve Chand; Alison Cloutier; Jonathon Davito; Chris Fjell; Tony Gaige; Detlev Ganten; Noreen Girn; Kurtis Guggenheimer; Heinz Himmelbauer; Thomas Kreitler; Stephen Leach; Darlene Lee; Hans Lehrach; Michael Mayo; Kelly Mead; Teika Olson; Pawan Pandoh; Anna-Liisa Prabhu; Heesun Shin; Simone Tänzer; Jason Thompson; Miranda Tsai; Jason Walker; George Yang; Mandeep Sekhon; LaDeana Hillier; Heike Zimdahl; Andre Marziali; Kazutoyo Osoegawa; Shaying Zhao; Asim Siddiqui; Pieter J de Jong; Wes Warren; Elaine Mardis; John D McPherson; Richard Wilson; Norbert Hübner; Steven Jones; Marco Marra; Jacqueline Schein
Journal:  Genome Res       Date:  2004-04       Impact factor: 9.043

4.  Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans.

Authors:  Jacqueline E Schein; Kristin L Tangen; Readman Chiu; Heesun Shin; Klaus B Lengeler; William Kim MacDonald; Ian Bosdet; Joseph Heitman; Steven J M Jones; Marco A Marra; James W Kronstad
Journal:  Genome Res       Date:  2002-09       Impact factor: 9.043

5.  Integrating sequence with FPC fingerprint maps.

Authors:  William Nelson; Carol Soderlund
Journal:  Nucleic Acids Res       Date:  2009-01-30       Impact factor: 16.971

6.  A sequence-based survey of the complex structural organization of tumor genomes.

Authors:  Benjamin J Raphael; Stanislav Volik; Peng Yu; Chunxiao Wu; Guiqing Huang; Elena V Linardopoulou; Barbara J Trask; Frederic Waldman; Joseph Costello; Kenneth J Pienta; Gordon B Mills; Krystyna Bajsarowicz; Yasuko Kobayashi; Shivaranjani Sridharan; Pamela L Paris; Quanzhou Tao; Sarah J Aerni; Raymond P Brown; Ali Bashir; Joe W Gray; Jan-Fang Cheng; Pieter de Jong; Mikhail Nefedov; Thomas Ried; Hesed M Padilla-Nash; Colin C Collins
Journal:  Genome Biol       Date:  2008-03-25       Impact factor: 13.583
  6 in total

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