Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.
Our variant ascertainment algorithm, VAAL, uses massively parallel DNA sequence data to identify differences between bacterial genomes with high sensitivity and specificity. VAAL detected approximately 98% of differences (including large insertion-deletions) between pairs of strains from three species while calling no false positives. VAAL also pinpointed a single mutation between Vibrio cholerae genomes, identifying an antibiotic's site of action by identifying sequence differences between drug-sensitive strains and drug-resistant derivatives.
15 references, click to expand
-
Whole-genome sequencing and variant discovery in C. elegans.Nat Methods. 2008 Feb;5(2):183-8 PMID: 18204455
-
Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor.Proc Natl Acad Sci U S A. 2006 May 23;103(21):8107-12 PMID: 16707573
-
Genomics and microbiology. Microbial forensics--"cross-examining pathogens".Science. 2002 Jun 14;296(5575):1976-9 PMID: 12004075
-
Quality scores and SNP detection in sequencing-by-synthesis systems.Genome Res. 2008 May;18(5):763-70 PMID: 18212088
-
Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori.Nat Methods. 2005 Dec;2(12):951-3 PMID: 16299480
-
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.Nat Genet. 2008 Aug;40(8):987-93 PMID: 18660809
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores.Genome Res. 2008 Nov;18(11):1851-8 PMID: 18714091
-
Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.Nature. 1999 Jan 14;397(6715):176-80 PMID: 9923682
-
ALLPATHS: de novo assembly of whole-genome shotgun microreads.Genome Res. 2008 May;18(5):810-20 PMID: 18340039
-
Microbiology. TB--a new target, a new drug.Science. 2005 Jan 14;307(5707):214-5 PMID: 15653490
-
Accurate whole human genome sequencing using reversible terminator chemistry.Nature. 2008 Nov 6;456(7218):53-9 PMID: 18987734
-
An Eulerian path approach to DNA fragment assembly.Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9748-53 PMID: 11504945
-
Single-molecule DNA sequencing of a viral genome.Science. 2008 Apr 4;320(5872):106-9 PMID: 18388294
-
Accurate multiplex polony sequencing of an evolved bacterial genome.Science. 2005 Sep 9;309(5741):1728-32 PMID: 16081699
-
Gene sequencing. The race for the $1000 genome.Science. 2006 Mar 17;311(5767):1544-6 PMID: 16543431
Contact
No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong
Qilu Normal University · Genelibs Bioinformatics Lab
750 Shunhua Rd, Jinan
2F, Bldg F, University Science Park
Tel: 0531-88819269
WeChat Official Account
Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.
Business Email
E-mail: [email protected]
Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2
