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Sipros specifications

Information


Unique identifier OMICS_06904
Name Sipros
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
Parallelization OpenMP
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for Sipros

Sipros citations

 (8)
library_books

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy P Framework

2018
Proteomes
PMCID: 5874766
PMID: 29385081
DOI: 10.3390/proteomes6010007

[…] encing, we considered two approaches. One is the recently described Omega (overlap-graph metagenome assembler), a software tool for assembly of shotgun metagenome data that can be used along with the Sipros algorithm for database generation and matching to MS/MS data []. The second was a novel method and software (called Sixgill) described by May et al. that uses a ‘metapeptide database’ derived f […]

library_books

Phylogenetically conserved resource partitioning in the coastal microbial loop

2017
PMCID: 5702734
PMID: 28800138
DOI: 10.1038/ismej.2017.128

[…] der the PRIDE archive PXD002641.The final database used for SIP searches (60 006 CDS) was constructed from all CDS with at least one peptide identification in regular (that is, unlabeled search mode) Sipros searches of each metaproteome against the 391 847 CDS from the full metagenome assembly and a reduced database consisting of 181 704 CDS from only high metagenome coverage contigs. To ensure su […]

library_books

Protein S drives oral squamous cell carcinoma tumorigenicity through regulation of AXL

2017
Oncotarget
PMCID: 5355156
PMID: 28118606
DOI: 10.18632/oncotarget.14753

[…] tibule. Purified human PROS1 protein was purchased from Enzyme Research Laboratories (South Bend, IN). R428 was purchased from SYNkinase. SCC cell lines were transiently transfected with PROS1 siRNA (siPROS1; ON-TARGETplus, SMARTpool # L-004833; Dharmacon) or with non-targeting siRNA (siNT ON-TARGETplus, SMARTpool #D-001810; Dharmacon) using DharmaFECT transfection reagent according to the manufac […]

library_books

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

2016
Front Microbiol
PMCID: 4850331
PMID: 27199908
DOI: 10.3389/fmicb.2016.00563

[…] from sample #3731 also exhibited a small but detectable isotopic enrichment of the protein pool during the 326-day incubation. The 15N atom % enrichment of the entire #3731 15N peptide pool based on Sipros analysis was 0.4% at T17d, increasing to 0.8% at T326d (while corresponding values for 14N control incubations were 0.5 and 0.4%, respectively).Peptides recovered from sample #5133 15N after 16 […]

library_books

Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

2016
mSystems
PMCID: 5069745
PMID: 27822523
DOI: 10.1128/mSystems.00027-15

[…] bases comprised of protein sequences from isolate marine microbes and metagenomes generated for the MB samples were constructed for confident identification of peptide spectral matches (PSM) with the Sipros program (, , ). All searches considered tryptic peptides in the range of 6 to 60 amino acids with a maximum of two missed cuts. Parent ion and fragment ion mass tolerances were 0.05 Da and 0.02 […]

library_books

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage

2016
Front Microbiol
PMCID: 4776211
PMID: 26973616
DOI: 10.3389/fmicb.2016.00238

[…] All MS/MS spectra were searched with Sipros (Pan et al., ; Hyatt and Pan, ; Wang et al., ) against a database containing ~80,000 proteins derived from ~80 Gb of genomic information obtained from previous genomic characterizations of biof […]

Citations

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Sipros institution(s)
BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA

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