A Greedy Algorithm for Aligning DNA Sequences

Zhang, Zheng; Schwartz, Scott; Wagner, Lukas; Miller, Webb

doi:10.1089/10665270050081478

Cited by 4,576 publications

(3,318 citation statements)

References 21 publications

Supporting

Mentioning

3,157

Contrasting

Unclassified

Order By: Relevance

“…The complete sequences of all segments of each isolate were compared using the Basic Local Alignment Search Tool (BLAST) to identify the most closely related sequences available in public databases 35. The nucleotide sequences of each gene segment were aligned using clc genomics workbench version 7.6 (Qiagen, Aarhus, Denmark), and the percentage nucleotide similarity was calculated using the MegAlign program of the dnastar package (DNASTAR, Inc., Madison, WI, USA).…”

Section: Methodsmentioning

confidence: 99%

Migratory birds in southern Brazil are a source of multiple avian influenza virus subtypes

Araújo

Petry

Fabrizio

et al. 2017

Influenza Resp Viruses

View full text Add to dashboard Cite

BackgroundThere is insufficient knowledge about the relation of avian influenza virus (AIV) to migratory birds in South America. Accordingly, we studied samples obtained over a 4‐year period (2009‐2012) from wild birds at a major wintering site in southern Brazil.MethodsWe obtained 1212 oropharyngeal/cloacal samples from wild birds at Lagoa do Peixe National Park and screened them for influenza A virus by RT‐PCR amplification of the matrix gene. Virus isolates were subjected to genomic sequencing and antigenic characterization.ResultsForty‐eight samples of 1212 (3.96%) contained detectable influenza virus RNA. Partial viral sequences were obtained from 12 of these samples, showing the presence of H2N2 (1), H6Nx (1), H6N1 (8), H9N2 (1), and H12N5 (1) viruses. As H6 viruses predominated, we generated complete genomes from all 9 H6 viruses. Phylogenetic analyses showed that they were most similar to viruses of South American lineage. The H6N1 viruses caused no disease signs in infected ferrets and, despite genetic differences, were antigenically similar to North American isolates.ConclusionsLagoa do Peixe National Park is a source of multiple AIV subtypes, with the levels of influenza virus in birds being highest at the end of their wintering period in this region. H6N1 viruses were the predominant subtype identified. These viruses were more similar to viruses of South American lineage than to those of North American lineage.

show abstract

Section: Methodsmentioning

confidence: 99%

Migratory birds in southern Brazil are a source of multiple avian influenza virus subtypes

Araújo

Petry

Fabrizio

et al. 2017

Influenza Resp Viruses

View full text Add to dashboard Cite

show abstract

“…The 33‐ to 64‐bp nucleotide sequences (hereafter “tags”) flanking sequenced ApeKI restriction sites associated with these SNPs were used in a BLASTALL v2.2.26 (Zhang et al. 2000) blastn search against an un‐annotated, normalized, 33.2‐Mbp expressed sequence tag (EST) library assembly derived from a single North American A. artemisiifolia individual collected in Minnesota (Lai et al. 2012), using an E‐value threshold of 10 −10 and reporting at most five best hits.…”

Section: Methodsmentioning

confidence: 99%

The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

Martin

Olsen

Samaniego

et al. 2016

Ecology and Evolution

View full text Add to dashboard Cite

Common ragweed (Ambrosia artemisiifolia L.) is an invasive, wind‐pollinated plant nearly ubiquitous in disturbed sites in its eastern North American native range and present across growing portions of Europe, Africa, Asia, and Australia. Phenotypic divergence between European and native‐range populations has been described as rapid evolution. However, a recent study demonstrated major human‐mediated shifts in ragweed genetic structure before introduction to Europe and suggested that native‐range genetic structure and local adaptation might fully explain accelerated growth and other invasive characteristics of introduced populations. Genomic differentiation that potentially influenced this structure has not yet been investigated, and it remains unclear whether substantial admixture during historical disturbance of the native range contributed to the development of invasiveness in introduced European ragweed populations. To investigate fine‐scale population genetic structure across the species' native range, we characterized diallelic SNP loci via a reduced‐representation genotyping‐by‐sequencing (GBS) approach. We corroborate phylogeographic domains previously discovered using traditional sequencing methods, while demonstrating increased power to resolve weak genetic structure in this highly admixed plant species. By identifying exome polymorphisms underlying genetic differentiation, we suggest that geographic differentiation of this important invasive species has occurred more often within pathways that regulate growth and response to defense and stress, which may be associated with survival in North America's diverse climatic regions.

show abstract

“…Both observations are attributable to the alignment algorithm used. First, the shorter local alignments are caused by the extension algorithm of the local alignment program, which extends the alignment only as long as the score does not drop by a certain value below the previous maximal score by aligning further bases [22,24]. The extension of the alignment will therefore stop earlier if the target genome is more distantly related, thus leading to shorter local alignments.…”

Section: Resultsmentioning

confidence: 99%

“…While necessity has required the use of fast local alignment programs such as BLAST [23], Mega BLAST [24] or BLASTZ [25] when handling such large datasets, the exact classification and filtering regimes have not been standardized or even comprehensively examined. In the most straight-forward classification scheme, reads that match a specific target genome with sufficient similarity are classified as endogenous (that is, from the target species) [11,13].…”

Section: Introductionmentioning

confidence: 99%