SOSUI protocols

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SOSUI specifications

Information


Unique identifier OMICS_07263
Name SOSUI
Interface Web user interface
Restrictions to use None
Input data A protein sequence
Output data Membrane proteins
Computer skills Basic
Stability Stable
Maintained Yes

Publications for SOSUI

SOSUI in pipelines

 (11)
2017
PMCID: 5573395
PMID: 28842677
DOI: 10.1038/s41598-017-09772-3

[…] of an intact na+/h+ exchanger domain (pfam: pf00999) by pfam (http://pfam.xfam.org/), and were named according to their similarity to arabidopsis homologous genes and phylogenetic relationship. sosui (http://harrier.nagahama-i-bio.ac.jp/sosui/sosui_submit.html) and psort (http://psort.hgc.jp/) were used to predict transmembrane domains and protein localization, respectively., […]

2016
PMCID: 4964579
PMID: 27464714
DOI: 10.1038/srep30542

[…] was derived using clustal w with default parameters. protein domains were predicted by the pfam protein families database. the transmembrane domains with hydrophobic residues were predicted by the sosui algorithm., to screen wcr active targets, 400 to 800 base pair regions of randomly selected non- redundant cdna clones were amplified using taq dna polymerase with a pair of gene specific […]

2016
PMCID: 5095628
PMID: 27430258
DOI: 10.1292/jvms.16-0264

[…] molecular weight (mw) and isoelectric point (pi) of protein were calculated by compute pi/mw tool (http://web.expasy.org/compute_pi/) []. the transmembrane region of hn protein was predicted by the sosui system (http://harrier.nagahama-i-bio.ac.jp/sosui/sosui_submit.html) []. the alignment of nt and deduced amino acid (aa) sequences and calculation of evolutionary distance in nt substitutions […]

2015
PMCID: 4641336
PMID: 26561515
DOI: 10.1186/s40793-015-0084-z

[…] of the genomic sequences was completed using the ncbi prokaryotic genome annotation pipeline which was combined using best-placed reference protein set and the gene caller genemarks+. signalp [] and sosui [] were used to predict signal peptides and transmembrane helices. the predicted cdss were also used to search against the pfam protein family database []. the genbank database [] and the cog […]

2014
PMCID: 3991678
PMID: 24748046
DOI: 10.1371/journal.pone.0095118

[…] was also carried out using the clustalw program available at ddbj (http://www.ddbj.nig.ac.jp/). a phylogenetic tree was built using dendroscope. tm domains of the ppklrs were predicted using the sosui program (http://bp.nuap.nagoya-u.ac.jp/sosui/)., y190 strain yeast was grown on ypd medium [10 g/l yeast extract (nakalai tesque, kyoto, japan), 20 g/l peptone (nakalai tesque), and 20 g/l […]


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SOSUI in publications

 (259)
PMCID: 5943349
PMID: 29743532
DOI: 10.1038/s41598-018-25388-7

[…] (ge healthcare). full-length cdnas were cloned using the smart race cdna amplification kit (clontech)., ncbi-blastp (http://blast.ncbi.nlm.nih.gov/blast.cgi), pfam (http://pfam.sanger.ac.uk/), and sosui (http://harrier.nagahama-i-bio.ac.jp/sosui/) were used to search for motifs in the nsd-1 sequence., recombinant autographa californica multiple nucleopolyhedroviruses (acmnpvs) were constructed […]

PMCID: 5784254
PMID: 29362235
DOI: 10.1128/mBio.02119-17

[…] for protein domain composition using the smart database () and pfam, prints, and tigrfams under interproscan (). tm domains were predicted using phobius (), tmhmm (), hmmtop (), gpcrhmm (), and sosui (). proteins containing domains other than pipk at the c terminus and those without tm domains were discarded. newly identified gpcr-pipks were then used in queries for iterative searches using […]

PMCID: 5773734
PMID: 29348349
DOI: 10.1128/genomeA.01480-17

[…] it shares an average nucleotide identity (ani) of 73% (genbank accession number ku530220)., abt2graduatex2 gp29 has been identified as a putative class ii holin () by structural homology () and sosui analysis showing two transmembrane regions (). abt2graduatex2 gp29 is present in all current members of the bg cluster, where it forms a putative operon with gp28, a lysin, but it is absent […]

PMCID: 5773202
PMID: 29346439
DOI: 10.1371/journal.pone.0191512

[…] intact if they revealed an open reading frame as well as intact splice sites., the amino acid sequences of the feline clca3 were analyzed in silico using the signalp 4.1 [], kyte–doolittle [], sosui [], hmmtop [], das [], psort ii [] and netnglyc (http://www.cbs.dtu.dk/services/netnglyc) software. putative proteolytic cleavage sites were identified by interspecies comparison of the amino […]


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SOSUI institution(s)
Tokyo University of Agriculture and Technology, Faculty of Technology, Department of Biotechnology, Tokyo, Japan; Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
SOSUI funding source(s)
This study was partly supported by a grant-in-aid for special projects in genome science from the Ministry of Education, Sports, Science and Technology.

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