SDT 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

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Publication for Sequence Demarcation Tool

SDT IN pipelines

 (5)
2017
PMCID: 5518176
PMID: 28744371
DOI: 10.1093/ve/vex017

[…] walking at macrogen inc. (south korea)., to investigate the anellovirus diversity detected in seals, the pairwise identities of the anellovirus genomes and orf1 sequences were determined using sdt v1.2 (muhire et al. 2014). all anellovirus sequences with a detectable complete orf1 were downloaded from genbank (on the 18th of march 2017). 727 orf1 sequences (including 152 from this study) […]

2017
PMCID: 5632515
PMID: 29026649
DOI: 10.1093/ve/vex027

[…] were predicted using a custom, papillomavirus-specific annotation tool as described previously (van doorslaer et al. 2013). genome-wide identity analysis was performed using default settings within sdt v1.2 (muhire et al. 2014). pairwise sequence comparisons with papv1 (varsani et al. 2014) were performed within geneious version 10.2 (kearse et al. 2012). the annotated sequence of papv1 […]

2016
PMCID: 4759964
PMID: 26895627
DOI: 10.1186/s12917-016-0657-0

[…] analysis were performed with geneious 8.0.5 (biomatters, auckland, new zealand). phylogenetic analyses were realized using mega 6.0 [22]. a nucleotide sequence identity matrix was produced with sequence demarcation tool version 1.2 [23]., a confirmation pcr was used to verify a point mutation in ns1 coding sequence. primers (tableĀ 3) were designed using primer3 [24]. pcrs were performed […]

2016
PMCID: 5013663
PMID: 27577948
DOI: 10.1038/ncomms12644

[…] kit (epoch life science, usa), and the purified product was sanger sequenced at macrogen (seoul, korea). the resulting sequence reads were checked and edited using mega46 version 5., we then used sequence demarcation tool47 v.1.2 to calculate pairwise similarity for each pair of aligned sequences, and used muscle48 to re-align the sequences and cluster them based on similarity scores, using […]

2015
PMCID: 4498126
PMID: 26217327
DOI: 10.3389/fmicb.2015.00696

[…] only conserved protein among cress-dna viruses (ilyina and koonin, 1992; rosario et al., 2012a) this protein was used to compare the different genomes. rep pairwise identities were calculated using sdt v1.2 (muhire et al., 2014) and summarized using heat maps generated in r (r core team, 2014). a maximum likelihood (ml) phylogenetic tree based on rep amino acid sequences was also constructed. […]

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

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