Base-Calling of Automated Sequencer Traces Using<i>Phred.</i> I. Accuracy Assessment

Ewing, Brent; Hillier, LaDeana W.; Wendl, Michael C.; Green, Phil

doi:10.1101/gr.8.3.175

Cited by 6,165 publications

(3,683 citation statements)

References 15 publications

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“…We closed the gap corresponding to the membrane-spanning repeat region of tolA with Sanger sequencing, using Phred/Phrap/Consed [39-41] to assemble and manually examine the sequence. Although the remaining two gaps were short, secondary structure arising from long palindromes impaired Sanger sequencing.…”

Section: Methodsmentioning

confidence: 99%

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Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

Williams

Wernegreen

2010

BMC Genomics

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BackgroundBlochmannia are obligately intracellular bacterial mutualists of ants of the tribe Camponotini. Blochmannia perform key nutritional functions for the host, including synthesis of several essential amino acids. We used Illumina technology to sequence the genome of Blochmannia associated with Camponotus vafer.ResultsAlthough Blochmannia vafer retains many nutritional functions, it is missing glutamine synthetase (glnA), a component of the nitrogen recycling pathway encoded by the previously sequenced B. floridanus and B. pennsylvanicus. With the exception of Ureaplasma, B. vafer is the only sequenced bacterium to date that encodes urease but lacks the ability to assimilate ammonia into glutamine or glutamate. Loss of glnA occurred in a deletion hotspot near the putative replication origin. Overall, compared to the likely gene set of their common ancestor, 31 genes are missing or eroded in B. vafer, compared to 28 in B. floridanus and four in B. pennsylvanicus. Three genes (queA, visC and yggS) show convergent loss or erosion, suggesting relaxed selection for their functions. Eight B. vafer genes contain frameshifts in homopolymeric tracts that may be corrected by transcriptional slippage. Two of these encode DNA replication proteins: dnaX, which we infer is also frameshifted in B. floridanus, and dnaG.ConclusionsComparing the B. vafer genome with B. pennsylvanicus and B. floridanus refines the core genes shared within the mutualist group, thereby clarifying functions required across ant host species. This third genome also allows us to track gene loss and erosion in a phylogenetic context to more fully understand processes of genome reduction.

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Section: Methodsmentioning

confidence: 99%

“…The resulting amplicons include the complete coding sequence of rpoZ and the intergenic sequence corresponding to the former location of glnA . We sequenced the amplified region using Sanger sequencing and assembled the reads with Phred/Phrap/Consed [39-41]. We also sequenced trpE from all of these B. vafer except strain 21.…”

Section: Methodsmentioning

confidence: 99%

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

Williams

Wernegreen

2010

BMC Genomics

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“…Consed, Phred, and Phrap are a free suite of programs that run on both Mac and Linux and can be used to automate base calling and quality control from sequence traces, assemble sequences, and edit sequence assemblies (Gordon et al., 1998; Ewing and Green, 1998; Ewing et al., 1998; http://www.phrap.org/phredphrapconsed.html). Additionally, there are several relatively inexpensive programs, such as ChromasPro (Technelysium, South Brisbane, Australia; Windows and Mac, used in this study) and Geneious (Biomatters Ltd., Auckland, New Zealand; Mac, Windows, and Linux), that can be used for contig assembly from traces and that allow manual editing of base calls.…”

Section: Data Management and Processingmentioning

confidence: 99%

Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia

et al. 2018

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The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost‐effective generation of high‐quality sequence data has transformed many fields, including those focused on discovering species and surveying biodiversity, monitoring movement of biological materials, forensic biology, and disease diagnostics. There is a need to build capacity to generate useful sequence data in countries with limited historical access to laboratory resources, so that researchers can benefit from the advantages offered by these data. Commonly used molecular techniques such as DNA extraction, PCR, and DNA sequencing are within the reach of small laboratories in many countries, with the main obstacles to successful implementation being lack of funding and limited practical experience. Here we describe a successful approach that we developed to obtain DNA sequence data during a small DNA barcoding project in Indonesia.

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“…Approximately 250 double-stranded, 3 Kb plasmid subclones were sequenced from both ends (ABI 3100 DNA Sequencer, Applied Biosystems, Inc., Foster City, CA, USA), and the contiguous sequences were assembled to obtain the full resistin gene sequence using the PHRED and PHRAP programs [16,17]. Thirty evenly-spaced sequence tagged sites were screened in 24 representative hypertensive study participants (50% Male, 50% Female; 50% Chinese, 50% Japanese).…”

Section: Snp Identificationmentioning

confidence: 99%

Absence of evidence for an association between resistin gene variants and insulin resistance in an Asian population with low and high blood pressure

Kimbell

Koropatnick

Grove

et al. 2008

Diabetes Research and Clinical Practice

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Aims-Although the function of resistin in human biology is unclear, some evidence suggests resistin gene variants influence insulin resistance, and insulin resistance-related hypertension. We searched for associations between common resistin gene variants and factors related to insulin resistance in Asian individuals with high or low blood pressure.Methods-Non-diabetic Chinese or Japanese sibling pairs were included if one had extreme hypertension and the other was either hypertensive or hypotensive. Four common, non-coding single nucleotide polymorphisms (SNPs) were identified by sequencing the resistin gene in 24 hypertensive probands. Generalized estimating equations-based regressions were then performed to test for SNP associations using the entire study population (n=1556).Results-Of 72 tests, only one was significant at the 0.05 level; 3.5 significant tests were expected by chance alone. High variability in insulin and triglyceride levels created wide confidence intervals, thus the negative results are not conclusive for these phenotypes. However, the large sample size resulted in narrow confidence intervals for BMI, fasting and 120 minute post-load glucose, and high and low density lipoprotein cholesterol. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Conflict of interest statementThe authors declare that they have no conflict of interest NIH Public Access Conclusion-Factors associated with insulin resistance are not likely influenced by the resistin gene in non-diabetic Asian individuals with high and low blood pressure.

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Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment

Cited by 6,165 publications

References 15 publications

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia

Absence of evidence for an association between resistin gene variants and insulin resistance in an Asian population with low and high blood pressure

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