XSTREAM protocols

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XSTREAM specifications

Information


Unique identifier OMICS_10036
Name XSTREAM
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Protein or nucleotide sequences
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline XSTREAM <>

Information


Unique identifier OMICS_10036
Name XSTREAM
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Protein or nucleotide sequences
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline XSTREAM <>

Publication for XSTREAM

XSTREAM in pipelines

 (6)
2017
PMCID: 5348893
PMID: 28288560
DOI: 10.1186/s12862-017-0927-x

[…] that were not in the n or c-termini and were low in alanine and glycine and were manually aligned. two authors (jvh and cyh) independently assigned spacer regions. tandem repeats were identified by xstream v1.4.8 using default parameters for moderate repeat degeneracy and high significance []., transcript abundance was estimated by aligning raw rna-seq reads [] (srr1539569 and srr1539569 for l. […]

2017
PMCID: 5400390
PMID: 28053006
DOI: 10.1093/molbev/msw294

[…] was chosen as the significant threshold. heatmaps were built using the heatmap.2 function in the gplots r package ()., secreted gene families were screened for the presence of rlcds by using xstream v1.73 software () with the following parameters: minimum character identity: 0.7; minimum tr domain length: 10 amino acids; minimum period: 1; and maximum gaps: 3. shematrin and krmp […]

2014
PMCID: 4177990
PMID: 25255291
DOI: 10.1371/journal.ppat.1004391

[…] clones of gp-hyp-1 -2 and -3 genes. for each subfamily, the middle region of the protein (between the two introns) was translated so that frame would be consistent with a cdna clone. the software xstream (http://jimcooperlab.mcdb.ucsb.edu/xstream/2013-8-8) was used to analyse the tandem repeats present for each subfamily. putative signal peptides and transmembrane domains were predicted using […]

2013
PMCID: 3662610
PMID: 23688042
DOI: 10.1186/1475-2875-12-165

[…] were confirmed by sequencing using an abi prism 310 genetic analyzer (pe applied biosystems, california, usa). vcg-1 strain pvarp was characterized in silico using signalp 3.0 [], fraganchor [], xstream [], tools and the interpro database [] to search for secretion signal or gpi-anchor sequences, tandem repeats and putative domains, respectively. clustal w software was used for aligning […]

2012
PMCID: 3382249
PMID: 22761664
DOI: 10.1371/journal.pone.0038084

[…] non-spider outgroup. thus, rooting of the spidroin gene tree was based on the minimization of total gene duplications plus losses., tandem repeats in spidroin protein sequences were identified using xstream under default settings and by eye. consensus repeat sequences and their lengths for each spidroin were determined based on 50% majority rule with ambiguities indicated by an x (). we also […]


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XSTREAM in publications

 (31)
PMCID: 5839467
PMID: 29520318
DOI: 10.1039/c7sc03236f

[…] r01 gm098304 to p. m. k. and r35 gm118044 to s. g. b. as well as a wallenberg academy fellowship to p. m. k. and a stanford bio-x fellowship to i. n. g. simulations were performed using the stanford xstream cluster, nsf blue waters, and the pdc center for high performance computing supported by the swedish national infrastructure for computing., available: and figures. see doi: […]

PMCID: 5523350
PMID: 28775897
DOI: 10.1155/2017/7259630

[…] were analyzed by using smart []. alpha helix and beta sheet were predicted by using psi pred server []. the presence of repeat was assessed by the sequence tandem repeat using the modeling software xstream []. mega 6 was implemented for phylogenetic tree construction []. the tertiary dimensional structure was predicted by using i-tasser standalone package []. for identification of probable […]

PMCID: 5468324
PMID: 28607350
DOI: 10.1038/s41598-017-03365-w

[…] percolation threshold. as shown in figure , the computational simulation for electrical conductivity started with designing an agnw/cmc composite with a composite modeling software (digimat-fe, e-xstream engineering). the digimat allows a user to create 3d representative volume element (rve) composed of a matrix phase filled with various filler material phases automatically. we created […]

PMCID: 5381272
PMID: 28378791
DOI: 10.1038/srep44578

[…] keri mckiernan for helpful comments on the manuscript. we thank the users of the [email protected] distributed computing project who donated compute time used for the simulations. this work also used the xstream computational resource, supported by the national science foundation major research instrumentation program (aci-1428930), and sherlock cluster. we would like to thank stanford university […]

PMCID: 5348893
PMID: 28288560
DOI: 10.1186/s12862-017-0927-x

[…] that were not in the n or c-termini and were low in alanine and glycine and were manually aligned. two authors (jvh and cyh) independently assigned spacer regions. tandem repeats were identified by xstream v1.4.8 using default parameters for moderate repeat degeneracy and high significance []., transcript abundance was estimated by aligning raw rna-seq reads [] (srr1539569 and srr1539569 for l. […]


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XSTREAM institution(s)
Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA

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