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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 citations

 (32)
library_books

Molecular Cloning and Characterization of Babesia orientalis Rhoptry Neck 2 BoRON2 Protein

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

[…] s 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 ancho […]

library_books

Conductive Cellulose Composites with Low Percolation Threshold for 3D Printed Electronics

2017
Sci Rep
PMCID: 5468324
PMID: 28607350
DOI: 10.1038/s41598-017-03365-w

[…] the 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 differe […]

library_books

Co Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity

2017
Mol Biol Evol
PMCID: 5400390
PMID: 28053006
DOI: 10.1093/molbev/msw294

[…] 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 proteins, […]

call_split

The full genome sequences of 8 equine herpesvirus type 4 isolates from horses in Japan

2016
PMCID: 5289262
PMID: 27840393
DOI: 10.1292/jvms.16-0506
call_split See protocol

[…] ORF24-R (5′-ccgcgcggtttatctgtagatcatattcaagttc-3′), ORF71-F (5′-ctacatcaacctcggtgtc-3′) and ORF71-R (5′-cctgtttgatccaaccgacc-3′). Direct repeat sequences were analyzed by Tandem Repeat Finder [] and XSTREAM [] and removed from sequences before multiple alignments. The locations of removal are indicated in . The whole genome, UL, US and IR of EHV-4s including sequences determined in the present st […]

library_books

Expansion of Lysine rich Repeats in Plasmodium Proteins Generates Novel Localization Sequences That Target the Periphery of the Host Erythrocyte*

2016
PMCID: 5207086
PMID: 27777305
DOI: 10.1074/jbc.M116.761213

[…] ino acids of ≥30 residues in length with with a lysine content of ≥20%. Within the set of lysine-rich sequence fragments, repeating protein sequences were identified using the tandem repeat predictor XSTREAM (). Parameters for XSTREAM were as follows: minimum word match = 0.6, minimum consensus match = 0.6, maximum period = 30, miss penalty = −3, and gap penalty = −3 (). Another custom perl script […]

library_books

Calmodulin Affects Sensitization of Drosophila melanogaster Odorant Receptors

2016
PMCID: 4751262
PMID: 26903813
DOI: 10.3389/fncel.2016.00028

[…] g/perfusion chamber (RC-27, Warner Instruments Inc., Hamden, CT, USA). Stimuli, consisting each of 10 μl of 50 μM VUAA1 or ethyl hexanoate in Ringer solution, were applied manually using a Multipette Xstream (Eppendorf, Hamburg, Germany) directly into the main inflow by means of a Y connector equipped with a flow valve. The dilution factor of the stimulus inside the chamber was equivalent to a 10− […]

Citations

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

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