Tablet—next generation sequence assembly visualization

Milne, Iain; Bayer, Micha; Cardle, Linda; Shaw, Paul; Stephen, Gordon; Wright, Frank; Marshall, David

doi:10.1093/bioinformatics/btp666

Cited by 602 publications

(483 citation statements)

References 6 publications

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“…Recombination events potentially involving other equine alphaherpesviruses were identified initially by viewing BWA alignments in Tablet (Milne et al., 2010), focusing on regions in which the sequence reads aligned poorly with the EHV‐1 references. Subsequent analysis of these regions using the program Simplot v.3.5.1 (Lole et al., 1999) produced sequence similarity plots that highlighted regions of possible recombination.…”

Section: Resultsmentioning

confidence: 99%

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Bryant

Wilkie

Russell

et al. 2018

Transbound Emerg Dis

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SummaryEquine herpesvirus 1 (EHV‐1) causes respiratory disease, abortion, neonatal death and neurological disease in equines and is endemic in most countries. The viral factors that influence EHV‐1 disease severity are poorly understood, and this has hampered vaccine development. However, the N752D substitution in the viral DNA polymerase catalytic subunit has been shown statistically to be associated with neurological disease. This has given rise to the term “neuropathic strain,” even though strains lacking the polymorphism have been recovered from cases of neurological disease. To broaden understanding of EHV‐1 diversity in the field, 78 EHV‐1 strains isolated over a period of 35 years were sequenced. The great majority of isolates originated from the United Kingdom and included in the collection were low passage isolates from respiratory, abortigenic and neurological outbreaks. Phylogenetic analysis of regions spanning 80% of the genome showed that up to 13 viral clades have been circulating in the United Kingdom and that most of these are continuing to circulate. Abortion isolates grouped into nine clades, and neurological isolates grouped into five. Most neurological isolates had the N752D substitution, whereas most abortion isolates did not, although three of the neurological isolates from linked outbreaks had a different polymorphism. Finally, bioinformatic analysis suggested that recombination has occurred between EHV‐1 clades, between EHV‐1 and equine herpesvirus 4, and between EHV‐1 and equine herpesvirus 8.

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Section: Resultsmentioning

confidence: 99%

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Bryant

Wilkie

Russell

et al. 2018

Transbound Emerg Dis

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“…Transcripts of at least 100 nt (LIB>100) or 70 nt (LIB<500, LIB<200) were considered further. The resulting transcripts from automatic classification were re-evaluated by visual inspection using Tablet 1.11.08.10 (Milne et al, 2010).…”

Section: Identification Of Intergenic Srnasmentioning

confidence: 99%

Genome‐wide identification of novel small RNAs in Pseudomonas aeruginosa

Gómez-Lozano

Marvig

Molin

et al. 2012

Environmental Microbiology

101

109

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Summary Bacterial small regulatory RNAs (sRNAs) function in post‐transcriptional control of gene expression and control a variety of processes including metabolic reactions, stress responses and pathogenesis in response to environmental signals. A variety of approaches have been used previously to identify 44 sRNAs in the opportunistic human pathogen Pseudomonas aeruginosa. In this work, RNA sequencing (RNA‐seq) is used to identify novel transcripts in P. aeruginosa involving a combination of three different sequencing libraries. Almost all known sRNAs and over 500 novel intergenic sRNAs are identified with this approach. Although the use of three libraries increased the number of novel transcripts identified, there were significant differences in the subset of transcripts detected in each library, underscoring the importance of library preparation strategy and relative sRNA abundance for successful sRNA detection. Nearly 90% of the novel sRNAs have no orthologous bacterial sequences outside of P. aeruginosa, supporting a limited degree of sequence conservation and rapid evolution of sRNAs at the species level. We anticipate that the data will be useful for the study of regulatory sRNAs in bacteria and that the approach described here may be applied to identify sRNAs in any bacterium under different growth and stress conditions.

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“…The main criterion for SSR identification was the minimum length, that is, eight repeat units for dinucleotides motif, six repeat units for trinucleotide and tetranucleotide, and four repeat units for pentanuclotide and other higherorder repeats. Sequences containing SSRs longer than 20 nucleotides were first reviewed with the use of Tablet (a next generation sequence assembly viewer) (Milne et al, 2010) in order to exclude all SSR-including sequences that were inappropriate for primer designing according to the following criteria: (a) very short DNA sequence flanking the microsatellite (less than 30 bases) or (b) microsatellite sequence repeat was used by assembler as an overlapping part for the adjacent reads, therefore, there is a probability that this contig is a chimeric one. Sequences were then aligned against National Center for Biotechnology Information (NCBI) non-redundant (nr) protein database using the BLASTX algorithm to determine the putative function (E < 1e-10).…”

Section: Identification Of Est-ssrs and Primer Designingmentioning

confidence: 99%

Identification and validation of novel EST-SSR markers in olives

Arbeiter

Hladnik

Jakše

et al. 2017

Sci. agric. (Piracicaba, Braz.)

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The olive (Olea europaea L.) is a leading oil crop in the Mediterranean area. Limited information on the inheritance of agronomic significant traits hinders progress in olive breeding programs, which encourages the development of markers linked to the traits. In this study, we report on the development of 46 olive simple sequence repeat (SSR) markers, obtained from 577,025 expressed sequence tags (ESTs) in developing olive fruits generated in the framework of the Slovenian national olive transcriptome project. Sequences were de novo assembled into 98,924 unigenes, which were then used as a source for microsatellites searching. We identified 923 unigenes that contained 984 SSRs among which dinucleotide SSRs (36 %) were the most abundant, followed by tri-(33 %) and hexa-(21 %) nucleotides. Microsatellite repeat motif GA (37 %) was the most common among dinucleotides, while microsatellite repeat motif GAA was the most abundant trinucleotide SSR motif (16 %). Gene ontology annotations could be assigned to 27 % of the unigenes. A hundred and ten expressed sequence tag-derived-simple sequence repeats (EST-SSRs) with annotated genes were selected for primer designing and finally, 46 (42 %) polymorphic EST-SSRs were successfully amplified and used to validate genetic diversity among 24 olive varieties. The average number of alleles per locus, observed heterozygosity, expected heterozygosity, and polymorphic information content were 4.5, 0.649, 0.604 and 0.539, respectively. Twenty-seven EST-SSRs showed good diversity properties and were recommended for further olive genome investigation.

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Tablet—next generation sequence assembly visualization

Cited by 602 publications

References 6 publications

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Genome‐wide identification of novel small RNAs in Pseudomonas aeruginosa

Identification and validation of novel EST-SSR markers in olives

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