Searching journal content for articles similar to Engler et al. 13 (9): 2152.

Displaying results 1-10 of 28

For checked items

view abstracts
download to citation manager

Select this article
Methods: SyMAP: A system for discovering and viewing syntenic regions of FPC maps
- Carol Soderlund,
- William Nelson,
- Austin Shoemaker,
- and Andrew Paterson
Genome Res. September 2006 16: 1159-1168; doi:10.1101/gr.5396706
...is recreated with the coordinates reversed for the second genomic sequence and the algorithm is run again to find the chains in the opposite orientation. Gregory et al. (2002) aligned mouse FPC contigs to the human minimal tiling path using mouse BESs, where they computed the anchors as BES matches with unique...
OPEN ACCESS ARTICLE
Select this article
Methods: Dynamic Building of a BAC Clone Tiling Path for the Rat Genome Sequencing Project
- Rui Chen,
- Erica Sodergren,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. April 2004 14: 679-684; doi:10.1101/gr.2171704
..., R.A., and Bradley, A. 2001 . A clone-array pooled shotgun strategy for sequencing large s. Genome Res. 11 : 1619 -1623. ↵ Engler, F.W., Hatfield, J., Nelson, W., and Soderlund, C.A. 2003 . Locating sequence on FPC maps and selecting a minimal tiling path. Genome Res. 13 : 2152 -2163. ↵ Gordon, D...
Select this article
METHODS: Contigs Built with Fingerprints, Markers, and FPC V4.7
- Carol Soderlund,
- Sean Humphray,
- Andrew Dunham,
- and Lisa French
Genome Res. November 1, 2000 10: 1772-1787; Published in Advance November 8, 2000, doi:10.1101/gr.GR-1375R
.... An * after a clone name indicates a parent clone. The clones highlighted in blue are the tiling path. The clone highlighted in cyan was selected with the mouse, which caused its markers and remarks to be highlighted in green and pink, respectively. The map units are the number of bands. New Features Recently...
Select this article
METHODS: Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species
- James W. Thomas,
- Arjun B. Prasad,
- Tyrone J. Summers,
- Shih-Queen Lee-Lin,
- Valerie V.B. Maduro,
- Jacquelyn R. Idol,
- Joseph F. Ryan,
- Pamela J. Thomas,
- Jennifer C. McDowell,
- and Eric D. Green
Genome Res. August 1, 2002 12: 1277-1285; doi:10.1101/gr.283202
.....washington.edu/UWGC/analysistools/segmap.cfm ), and the clone-overgo information was imported into FPC . The resulting contigs were examined manually, and minimally overlapping sets of clones (sequence-tiling paths) were selected based on the fingerprint and overgo-content data. Updated sequence-tiling paths can be viewed at www.nisc.nih.gov . WEB SITE...
Select this article
METHODS: Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome
- Alex Lim,
- Eileen T. Dimalanta,
- Konstantinos D. Potamousis,
- Galex Yen,
- Jennifer Apodoca,
- Chunhong Tao,
- Jieyi Lin,
- Rong Qi,
- John Skiadas,
- Arvind Ramanathan,
- Nicole T. Perna,
- Guy Plunkett III,
- Valerie Burland,
- Bob Mau,
- Jeremiah Hackett,
- Frederick R. Blattner,
- Thomas S. Anantharaman,
- Bhubaneswar Mishra,
- and David C. Schwartz
Genome Res. September 1, 2001 11: 1584-1593; Published in Advance August 16, 2001, doi:10.1101/gr.172101
...were digested (on optical mapping surfaces) with restriction endonucleases, and images were collected using Gencol (see Methods). The basis of how shotgun optical mapping assembles whole maps is similar in many ways to random clone mapping approaches that assemble tiling paths across chromosomes...
Select this article
RESOURCE: Physical Maps for Genome Analysis of Serotype A and D Strains of the Fungal Pathogen Cryptococcus neoformans
- 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,
- and James W. Kronstad
Genome Res. September 1, 2002 12: 1445-1453; Published in Advance August 21, 2002, doi:10.1101/gr.81002
...clone), then add those sizes to the cumulative size estimate; (3) repeat step 2 until all unique fragments in the tiling path clones have been identified and summed to give a total size estimate. Shared fragments are as defined by the FPC parameters used such that two fragments are considered the same...
Select this article
RESOURCE: A Marker-Dense Physical Map of the Bradyrhizobium japonicum Genome
- Jeffrey P. Tomkins,
- Todd C. Wood,
- Minviluz G. Stacey,
- John T. Loh,
- Adam Judd,
- Jose L. Goicoechea,
- Gary Stacey,
- Michael J. Sadowsky,
- and Rod A. Wing
Genome Res. August 1, 2001 11: 1434-1440; doi:10.1101/gr.185001
...analyzed, as shown in Figure 1 A. Results indicate that the average insert size is 146 kb with &gt;78% of the clones &gt;100 kb. View larger version: In this window In a new window Figure 3. Six FPC contigs illustrated by a selected set of BAC clones providing a complete tiling path of the Bradyrhizobium...
Select this article
Method: Sequence-based physical mapping of complex genomes by whole genome profiling
- Jan van Oeveren,
- Marjo de Ruiter,
- Taco Jesse,
- Hein van der Poel,
- Jifeng Tang,
- Feyruz Yalcin,
- Antoine Janssen,
- Hanne Volpin,
- Keith E. Stormo,
- Robert Bogden,
- Michiel J.T. van Eijk,
- and Marcel Prins
Genome Res. April 2011 21: 618-625; Published in Advance February 1, 2011, doi:10.1101/gr.112094.110
...-six percent (51,935 tags) of the theoretically possible 60,676 unique in silico tags were also retrieved in the wet-lab WGP experiment (Table 1). Contig building using FPC and map quality assessment A cut-off value of 1.03 10#2;6 and a consecutiveDQ stepwas used in the FingerPrinted Contig (FPC) software...
Select this article
RESOURCE: The Atlas Genome Assembly System
- Paul Havlak,
- Rui Chen,
- K. James Durbin,
- Amy Egan,
- Yanru Ren,
- Xing-Zhi Song,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. April 2004 14: 721-732; doi:10.1101/gr.2264004
...constructed using restriction enzyme digestion fingerprinting and specialized software ( Soderlund et al. 1997 ). A minimal tiling path is derived from the map, and each clone in the tiling path is shotgun-sequenced and assembled ( Kent and Haussler 2001 ; Choi and Farach-Colton 2003 ). The entire...
Select this article
Research: Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
- Gang Li,
- Brian W. Davis,
- Terje Raudsepp,
- Alison J. Pearks Wilkerson,
- Victor C. Mason,
- Malcolm Ferguson-Smith,
- Patricia C. O'Brien,
- Paul D. Waters,
- and William J. Murphy
Genome Res. September 2013 23: 1486-1495; Published in Advance June 20, 2013, doi:10.1101/gr.154286.112
...25 canine BAC clones and 18 feline BAC clones (Pearks Wilkerson et al. 2008) selected from minimum tiling paths were sheared to ;3-kb insert length and pooled in equimolar ratios to prepare 454 Life Sciences (Roche) FLX paired-end libraries. Pooled libraries for dog and cat were each sequenced...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Engler et al. 13 (9): 2152.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: