FAST: FAST Analysis of Sequences Toolbox

Lawrence, Travis J; Kauffman, Kyle T.; Amrine, Katherine C. H.; Carper, Dana L.; Lee, Raymond S.; Becich, Peter; Canales, Claudia J.; Ardell, David H.

doi:10.3389/fgene.2015.00172

Cited by 34 publications

(29 citation statements)

References 56 publications

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“…The parameters were fixed as follows: “–min: 2–20, –th1: 0.95, –par: 1 and –th2: 0.01” where min is the minimal number of reads to call a genotype, th1 the genotype posterior probability threshold, par the paraclean option (1 = activated), and th2 the paraclean LRT p ‐value threshold. The nucleotide diversity was assessed globally on the nine fasta format files (one for each sequenced individual) obtained with reads 2 snp using the alnpi program from the fast toolbox (Lawrence et al., , https://github.com/tlawrence3/FAST).…”

Section: Methodsmentioning

confidence: 99%

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

Verdu

Guichoux

Quevauvillers

et al. 2016

Ecology and Evolution

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The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.

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Section: Methodsmentioning

confidence: 99%

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

Verdu

Guichoux

Quevauvillers

et al. 2016

Ecology and Evolution

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“…Protein sequences were aligned with MUSCLE (71), and the corresponding DNA sequences were back translated to give a codon alignment. Population genetic statistics, including π n and Tajima's D, were calculated using Bioperl (72) and FAST (73). Duplicate sequences were removed, and then a maximum-likelihood phylogeny was generated using RAxML v7.0.3 with a general time-reversible substitution model and a gamma model of rate heterogeneity (74).…”

Section: Methodsmentioning

confidence: 99%

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening

Croucher

Campo

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

133

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Characterizing the immune response to pneumococcal proteins is critical in understanding this bacterium's epidemiology and vaccinology. Probing a custom-designed proteome microarray with sera from 35 healthy US adults revealed a continuous distribution of IgG affinities for 2,190 potential antigens from the species-wide pangenome. Reproducibly elevated IgG binding was elicited by 208 "antibody binding targets" (ABTs), which included 109 variants of the diverse pneumococcal surface proteins A and C (PspA and PspC) and zinc metalloprotease A and B (ZmpA and ZmpB) proteins. Functional analysis found ABTs were enriched in motifs for secretion and cell surface association, with extensive representation of cell wall synthesis machinery, adhesins, transporter solute-binding proteins, and degradative enzymes. ABTs were associated with stronger evidence for evolving under positive selection, although this varied between functional categories, as did rates of diversification through recombination. Particularly rapid variation was observed at some immunogenic accessory loci, including a phage protein and a phase-variable glycosyltransferase ubiquitous among the diverse set of genomic islands encoding the serine-rich PsrP glycoprotein. Nevertheless, many antigens were conserved in the core genome, and strains' antigenic profiles were generally stable. No strong evidence was found for any epistasis between antigens driving population dynamics, or redundancy between functionally similar accessory ABTs, or age stratification of antigen profiles. These results highlight the paradox of why substantial variation is observed in only a subset of epitopes. This result may indicate only some interactions between immunoglobulins and ABTs clear pneumococcal colonization or that acquired immunity to pneumococci is an accumulation of individually weak responses to ABTs evolving under different levels of functional constraint.genomics | pathogens | evolution | immunology | epidemiology

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“…We structurally aligned tRNA data using COVEA [52] with the TRNA2-prok.cm model from tRNAscan-SE v.1.23 [18] and analyzed feature statistics using FAST [53]. Complete commands to reproduce data in Tables 1, 2, 3 and 4 are provided in the Supplement.…”

Section: Methodsmentioning

confidence: 99%

Initiator tRNA genes template the 3′ CCA end at high frequencies in bacteria

Ardell

Hou

2016

BMC Genomics

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BackgroundWhile the CCA sequence at the mature 3′ end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and Archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In Bacteria, tRNA genes template CCA sporadically.ResultsIn order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database version 0.8. Among 132,129 prokaryotic tRNA genes, initiator tRNA genes template CCA at the highest average frequency (74.1%) over all functional classes except selenocysteine and pyrrolysine tRNA genes (88.1% and 100% respectively). Across bacterial phyla and a wide range of genome sizes, many lineages exist in which predominantly initiator tRNA genes template CCA. Convergent and parallel retention of CCA templating in initiator tRNA genes evolved in independent histories of reductive genome evolution in Bacteria. Also, in a majority of cyanobacterial and actinobacterial genera, predominantly initiator tRNA genes template CCA. We also found that a surprising fraction of archaeal tRNA genes template CCA.ConclusionsWe suggest that cotranscriptional synthesis of initiator tRNA CCA 3′ ends can complement inefficient processing of initiator tRNA precursors, “bootstrap” rapid initiation of protein synthesis from a non-growing state, or contribute to an increase in cellular growth rates by reducing overheads of mass and energy to maintain nonfunctional tRNA precursor pools. More generally, CCA templating in structurally non-conforming tRNA genes can afford cells robustness and greater plasticity to respond rapidly to environmental changes and stimuli.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3314-x) contains supplementary material, which is available to authorized users.

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FAST: FAST Analysis of Sequences Toolbox

Cited by 34 publications

References 56 publications

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening

Initiator tRNA genes template the 3′ CCA end at high frequencies in bacteria

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