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Protocols

SMS specifications

Information


Unique identifier OMICS_21166
Name SMS
Alternative name The Sequence Manipulation Suite
Interface Web user interface
Restrictions to use None
Programming languages Javascript
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Paul Stothard

Additional information


http://www.bioinformatics.org/sms/faq.html

Publication for The Sequence Manipulation Suite

SMS citations

 (34)
call_split

Early Archean origin of heterodimeric Photosystem I

2018
PMCID: 5857716
PMID: 29560463
DOI: 10.1016/j.heliyon.2018.e00548
call_split See protocol

[…] alignments were performed using Clustal Omega employing 10 combined guide trees and Hidden Markov Model iterations . The percentage of sequence identity between pair of sequences was estimated using the Sequence Manipulation Suite online service . The Maximum Likelihood tree using all retrieved sequences and shown in were calculated with PhyML 3.0 using the smart model selection option allowing […]

library_books

Investigating Potential Chromosomal Rearrangements during Laboratory Culture of Neisseria gonorrhoeae

2018
PMCID: 5874624
PMID: 29361673
DOI: 10.3390/microorganisms6010010

[…] N. gonorrhoeae strain NCCP11945 [] was analysed for the presence of SpeI restriction enzyme recognition sites, 5′-ACTAGT-3′ (), and BglII restriction enzyme recognition sites, 5′-AGATCT-3′ (), using the Sequence Manipulation Suite: DNA Pattern Find []. These enzymes were chosen based on previous PFGE and mapping experiments in other N. gonorrhoeae strains [,]. The predicted fragment sizes and the […]

call_split

Methods for detecting Gemmata spp. bacteremia in the microbiology laboratory

2018
BMC Res Notes
PMCID: 5759251
PMID: 29310696
DOI: 10.1186/s13104-017-3119-2
call_split See protocol

[…] w universal bacterial genes whose sequence has been shown to accurately identify closely related bacterial species []. Primers and probes were selected using primer3 software [, ], primerBlast [] and The Sequence Manipulation Suite []. Primers and probe specificity was tested in silico by a BLAST analysis against all sequences deposited in GenBank database (May, 2016). The specificity was then exp […]

call_split

Put3 Positively Regulates Proline Utilization in Candida albicans

2017
PMCID: 5729217
PMID: 29242833
DOI: 10.1128/mSphere.00354-17
call_split See protocol

[…] ut using Fungal Orthogroups Repository (https://portals.broadinstitute.org/regev/orthogroups/) (). Color coding of amino acid classes in the Put3 and ortholog sequences was done using an online tool, the Sequence Manipulation Suite (). A Newick file for Put3 yeast phylogeny was generated using Fungal Orthogroups Repository () and then modified and used to generate the Put3 phylogenetic tree using […]

library_books

Characterization of a Novel RNA Virus Discovered in the Autumnal Moth Epirrita autumnata in Sweden

2017
Viruses
PMCID: 5580471
DOI: 10.3390/v9080214

[…] re assist in virus host identification. The codon usage and dinucleotide frequencies for the different codon regions of the virus nucleotide sequences () were obtained at www.bioinformatics.org using the Sequence Manipulation Suite []. The dinucleotide frequency bias for each of the 16 dinucleotides was calculated as the ratio of the observed and expected dinucleotide frequencies, the latter being […]

library_books

Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

2017
Front Plant Sci
PMCID: 5415607
PMID: 28523013
DOI: 10.3389/fpls.2017.00709

[…] GLAM2 ().Dehydrin sequences were submitted to the EXPASY server’s isoelectric point (pI) and molecular mass (Mr) calculator to compute the theoretical pI and Mr (). GRAVY scores were calculated using the Sequence Manipulation Suite (). The molecular masses, pI values, GRAVY scores, and motif compositions were visualized in R using the bean plot package ().Patterns of dehydrin architecture were exa […]

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SMS institution(s)
Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada

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