Communication-minimal tiling of uniform dependence loops

1997 ◽  
pp. 330-349 ◽  
Author(s):  
Jingling Xue
Keyword(s):  
Minimal Tiling

scholarly journals Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource

BioTechniques ◽  
2004 ◽  
Vol 37 (2) ◽  
pp. 282-284 ◽  
Author(s):  
Volker Hollich ◽  
Eric Johnson ◽  
Eileen E. Furlong ◽  
Boris Beckmann ◽  
Joseph Carlson ◽  
...  
Keyword(s):  
Minimal Tiling Path ◽  
Genomic Clones ◽  
Common Resource ◽  
Minimal Tiling

scholarly journals A Comparative BAC Map for the Gilthead Sea Bream (Sparus aurataL.)

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Heiner Kuhl ◽  
Elena Sarropoulou ◽  
Mbaye Tine ◽  
Georgios Kotoulas ◽  
Antonios Magoulas ◽  
...  
Keyword(s):  
Gasterosteus Aculeatus ◽  
Sparus Aurata ◽  
Bac Library ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Insert Size ◽  
Marine Aquaculture ◽  
End Sequences ◽  
Minimal Tiling ◽  
Stickleback Genome

This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata), a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6 Mbp). Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus) genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5% of the stickleback chromosomes and 70.2% of the genes that have been annotated. The N50 size of 1,485 “BACtigs” consisting of redundant BACs is 337,253 bp. The largest BACtig covers 2.15 Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome.

Developing the Performance of Tiling Arrays

2012 ◽  
pp. 159-169
Author(s):  
Mohamed Abdelhamid Abbas
Keyword(s):  
Shortest Path ◽  
Tiling Array ◽  
Dijkstra’S Algorithm ◽  
A Algorithm ◽  
Average Complexity ◽  
Tiling Arrays ◽  
Dijkstra's Algorithm ◽  
Long Time ◽  
Search Approach ◽  
Minimal Tiling

Genomic tiling arrays are able to inspect the genome of haphazard species for which the sequence is known. The plan of proper oligonucleotide probes for such arrays is computationally difficult if features such as oligonucleotide quality and recurring regions are considered. Prior works have developed the minimal tiling path problem for the choice of oligonucleotides using Dijkstra’s shortest path algorithm to compute universal finest tiling paths from millions of candidate oligonucleotides on computers. Although Dijkstra’s algorithm works well, it is complicated and may take a long time for routers to process it and the efficiency of the network fails. In this paper, the author discusses a search approach that can decrease the average complexity time of tilling arrays. This aspiration is realized by searching for the shortest path to the probes using a faster algorithm. This paper enhances A* Algorithm and exploits the enhanced version, called A**, instead of Dijkstra’s algorithm. The enhanced version is more efficient and can decrease the average time complexity, thus increasing the performance of tiling array.

scholarly journals Swine Genome Sequencing Consortium (SGSC): A Strategic Roadmap for Sequencing The Pig Genome

2005 ◽  
Vol 6 (4) ◽  
pp. 251-255 ◽  
Author(s):  
Lawrence B. Schook ◽  
Jonathan E. Beever ◽  
Jane Rogers ◽  
Sean Humphray ◽  
Alan Archibald ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Mapping Data ◽  
The Past ◽  
Physical Maps ◽  
Genome Sequencing Consortium ◽  
Pig Genome ◽  
Sequencing Strategy ◽  
Bac End Sequencing ◽  
International Participation ◽  
Minimal Tiling

The Swine Genome Sequencing Consortium (SGSC) was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC’s mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP) that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA), presentations demonstrated that a human–pig comparative map has been completed, BAC fingerprint contigs (FPC) for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG) shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3x coverage of BACs comprising the MTP and 3x of the WG-shotgun libraries will be used to develop a draft 6x coverage of the pig genome.

A Minimal Tiling Path Cosmid Library for Functional Analysis of thePseudomonas aeruginosaPAO1 Genome

2000 ◽  
Vol 5 (4) ◽  
pp. 189-203 ◽  
Author(s):  
BIXING HUANG ◽  
CYNTHIA B. WHITCHURCH ◽  
LARRY CROFT ◽  
SCOTT A. BEATSON ◽  
JOHN S. MATTICK
Keyword(s):  
Functional Analysis ◽  
Cosmid Library ◽  
Minimal Tiling Path ◽  
Minimal Tiling
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