ArticleGenome research2006
Physical map-assisted whole-genome shotgun sequence assemblies.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed, 35 citations in OpenAlex.
- Extensive error in the number of genes inferred from draft genome assemblies.PLoS computational biology · 2014Article
- A first generation BAC-based physical map of the half-smooth tongue sole (Cynoglossus semilaevis) genome.BMC genomics · 2014Article
- Article
- SIS: a program to generate draft genome sequence scaffolds for prokaryotes.BMC bioinformatics · 2012Article
- Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome.BMC genomics · 2011Article
- Article
- Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries.BMC genomics · 2010Article
- Article
- A compartmentalized approach to the assembly of physical maps.BMC bioinformatics · 2009Article
- Automated FingerPrint Background removal: FPB.BMC bioinformatics · 2009Article
- Integrating sequence with FPC fingerprint maps.Nucleic acids research · 2009Article
- A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome.Genome biology · 2007Article
- A high utility integrated map of the pig genome.Genome biology · 2007Article
Corrections and comments
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Authors and funding
17 authors at 5 institutions in 2 countries.
Funding
Abstract
We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical maps. Clone sizes and overlaps derived from clone fingerprints are used for the calculation of length constraints between any two BAC neighbors sharing 40% of their size. These constraints are used to promote the linkage and guide the arrangement of sequence contigs within a sequence scaffold at the layout phase of WGS assemblies. This process is facilitated by FASSI, a stand-alone application that calculates BAC end and BAC overlap length constraints from clone fingerprint map contigs created by the FPC package. FASSI is designed to work with the assembly tool PCAP, but its output can be formatted to work with other WGS assembly algorithms able to use length constraints for individual clones. The FASSI method is simple to implement, potentially cost-effective, and has resulted in the increase of scaffold contiguity for both the Drosophila melanogaster and Cryptococcus gattii genomes when compared to a control assembly without map-derived constraints. A 6.5-fold coverage draft DNA sequence of the Pan troglodytes (chimpanzee) genome was assembled using map-derived constraints and resulted in a 26.1% increase in scaffold contiguity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.