SBASE protocols

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SBASE specifications

Information


Unique identifier OMICS_11878
Name SBASE
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Input format RAW
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Sandor Pongor <>

Publication for SBASE

SBASE in pipeline

2013
PMCID: 3856593
PMID: 24134787
DOI: 10.1186/1471-2164-14-710

[…] linear models and empirical bayes methods, and p values adjusted using the benjamini and hochberg's method to control for multiple testing. fully annotated microarray data have been deposited in bμ[email protected]sbase (accession number: e-bugs-150; http://bugs.sgul.ac.uk/e-bugs-150) and also arrayexpress (accession number: e-bugs-150)., whole genome paired end (2 x 76bp) sequencing was performed using […]


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SBASE in publications

 (82)
PMCID: 5895944
PMID: 29682286
DOI: 10.1302/2046-3758.72.BJR-2017-0078.R2

[…] kg., impactor tips with five different stiffnesses (stip ) were tested (tip 1 to tip 5, . see supplementary material for measurement of tip stiffness), with three different base plate stiffnesses sbase (‘soft’: 0.5 n/m, ‘stiff’: 5.0 n/m, ‘rigid’: >105 n/m) for two different impaction energies (ehigh=2.2 j, elow=1.1 j). 1.1 j is prescribed for similar testing of modular components […]

PMCID: 5814437
PMID: 29449573
DOI: 10.1038/s41598-018-21340-x

[…] termination method using an abi prism 477 dna sequencer (pe biosystems, foster city, ca, usa). the sequences were scanned against the genbank database blast (www.genome.jp/tools/clustalw/) and the sbase domain prediction system (www.icgeb.trieste.it/sbase/) programs., the b1 encoding sequence and all deletion fragments were cloned into pcdna3.1 (clontech, usa) or p3xflag-myc-cmv-26 vectors […]

PMCID: 5715130
PMID: 29089466
DOI: 10.1042/BSR20160614

[…] by ‘reverse evolution’ based on consensus dna sequences of different transposons derived from different fish species []. these pioneering efforts showed that the reverse-engineered sb transposase (sbase) could catalyze transposition of its cognate transposon dna []. nevertheless, the overall transposition efficiency remained low and insufficient for most gene therapy clinical applications. […]

PMCID: 5509696
PMID: 28706260
DOI: 10.1038/s41598-017-05689-z

[…] literature, and by using databases such as the human metabolome data base (hmdb): http://hmdb.ca/  , and the biological magnetic resonance data bank (bmrb) http://www.bmrb.wisc.edu/, along with sbase/amix (bruker biospin 2006) and nmr suite (chenomx, edmonton, canada)., dna was extracted from faecal and colonic content samples using the qiagen ez1 kit (qiagen, germany) after mechanical […]

PMCID: 5405179
PMID: 28373096
DOI: 10.1016/j.ebiom.2017.03.034

[…] statistical correlations were validated experimentally using 2d nmr spectra (a set of cosy, tocsy and 1h,13c–hsqc experiments were performed on selected samples) metabolites were then found in the sbase database using amix 3·9·11 software (bruker biospin, germany) or in published literature (, )., lipoprotein subclass analysis was performed using the 1d general profiling of serum samples […]


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SBASE institution(s)
Protein Structure and Bioinformatics, ICGEB, Trieste, Italy

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