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Protocols

SDT specifications

Information


Unique identifier OMICS_06325
Name SDT
Alternative name Sequence Demarcation Tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Sequence Demarcation Tool

SDT citations

 (57)
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Complete Genome Sequencing of a Novel Type of Omikronpapillomavirus 1 in Indian River Lagoon Bottlenose Dolphins (Tursiops truncatus)

2018
Genome Announc
PMCID: 5920176
PMID: 29700141
DOI: 10.1128/genomeA.00240-18
call_split See protocol

[…] phocoena) (), and Burmeister’s porpoise (Phocoena spinipinnis) (). The L1 gene sequence of the BDPV was compared to those of all cetacean PVs and the type species of the other 46 PV genera using the Sequence Demarcation Tool (). The BDPV displayed greatest nucleotide identity (75.8%) to OmikronPV1 (Tursiops truncatus papillomavirus 6 [TtPV6]) (). Given that this is the ninth PV type described fro […]

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Analysis of DNAs associated with coconut foliar decay disease implicates a unique single stranded DNA virus representing a new taxon

2018
Sci Rep
PMCID: 5890292
PMID: 29632309
DOI: 10.1038/s41598-018-23739-y
call_split See protocol

[…] reassembled, and the resulting contigs were checked by BLAST for known virus sequences and obvious contamination by plant, microbe or human sequences.Phylogenetic analyses were conducted in MEGA7 and SDT v. 1.2. Multialignments were done using Muscle as implemented in Geneious or MEGA7. A maximum likelihood tree (100 bootstrap repetitions) was constructed by PhyML with the GTR + G + I substitution […]

library_books

Passion Fruit Chlorotic Mottle Virus: Molecular Characterization of a New Divergent Geminivirus in Brazil

2018
Viruses
PMCID: 5923463
PMID: 29614801
DOI: 10.3390/v10040169

[…] rred using PHYML 3.0 [] and the tree was midpoint rooted. Braches with <0.8 aLRT support were collapsed using TreeGraph2 [].All pairwise identities (genome-wide, CP, MP and Rep) were determined using SDT v1.2 []. […]

library_books

Novel Parvoviruses from Wild and Domestic Animals in Brazil Provide New Insights into Parvovirus Distribution and Diversity

2018
Viruses
PMCID: 5923437
PMID: 29565808
DOI: 10.3390/v10040143

[…] as estimated via bootstrap replicates. Phylogenetic trees were visualized using Figtree 1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). Nucleotide divergence calculations were performed using the Sequence Demarcation Tool (SDT) version 1.2 in muscle mode []. […]

library_books

The Incidence and Genetic Diversity of Apple Mosaic Virus (ApMV) and Prune Dwarf Virus (PDV) in Prunus Species in Australia

2018
Viruses
PMCID: 5869529
PMID: 29562672
DOI: 10.3390/v10030136

[…] 1000 bootstrap replicates and the resulting trees were visualized in FigTree (version 1.4.2) []. Branches that had less than 50% bootstrap support were collapsed. Sequence identity analysis using the sequence demarcation tool (SDT) (version 1.2) [] was carried out on the aligned amplicon clusters of each viral RNA segment.Full length genome sequences of the Australian ApMV isolate K75 and PDV isol […]

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How Does Food Taste in Anorexia and Bulimia Nervosa? A Protocol for a Quasi Experimental, Cross Sectional Design to Investigate Taste Aversion or Increased Hedonic Valence of Food in Eating Disorders

2018
Front Psychol
PMCID: 5859071
PMID: 29593595
DOI: 10.3389/fpsyg.2018.00264
call_split See protocol

[…] p temporal-liking (MSTL) with taste reactivity (TR) task in study 2. Each experimental session will take around 1.5 h. Concerning the first study (Table ), the 2AFC test with signal detection theory (SDT) analysis will be used as it provides a high level of power for small food differences and low levels of response bias (Hautus et al., ). On the one hand, the 2AFC test is a psychophysical method […]

Citations

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SDT institution(s)
Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa

SDT review

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Nasim Ahmed

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Desktop
I use SDT for viruses classification. It works well and very informative data it generates.
Regards
Nasim