178,066 research outputs found
New pairs of m-sequences with 4-level cross-correlation
AbstractLet ω be a primitive element of GF(2n), where n≡0(mod4). Let d=(22k+2s+1-2k+1-1)/(2s-1), where n=2k, and s is such that 2s divides k. We prove that the binary m-sequences s(t)=tr(ωt) and s(dt) have a four-level cross-correlation function and give the distribution of the values
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
The standard approach to analyzing 16S tag sequence data, which relies on
clustering reads by sequence similarity into Operational Taxonomic Units
(OTUs), underexploits the accuracy of modern sequencing technology. We present
a clustering-free approach to multi-sample Illumina datasets that can identify
independent bacterial subpopulations regardless of the similarity of their 16S
tag sequences. Using published data from a longitudinal time-series study of
human tongue microbiota, we are able to resolve within standard 97% similarity
OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S
tags differing by as little as 1 nucleotide (99.2% similarity). A comparative
analysis of oral communities of two cohabiting individuals reveals that most
such subpopulations are shared between the two communities at 100% sequence
identity, and that dynamical similarity between subpopulations in one host is
strongly predictive of dynamical similarity between the same subpopulations in
the other host. Our method can also be applied to samples collected in
cross-sectional studies and can be used with the 454 sequencing platform. We
discuss how the sub-OTU resolution of our approach can provide new insight into
factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures +
supplement. Significantly revised for clarity, references added, results not
change
In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip(® )technology
BACKGROUND: Genomic approaches in large animal models (canine, ovine etc) are challenging due to insufficient genomic information for these species and the lack of availability of corresponding microarray platforms. To address this problem, we speculated that conserved interspecies genetic sequences can be experimentally detected by cross-species hybridization. The Affymetrix platform probe redundancy offers flexibility in selecting individual probes with high sequence similarities between related species for gene expression analysis. RESULTS: Gene expression profiles of 40 canine samples were generated using the human HG-U133A GeneChip (U133A). Due to interspecies genetic differences, only 14 ± 2% of canine transcripts were detected by U133A probe sets whereas profiling of 40 human samples detected 49 ± 6% of human transcripts. However, when these probe sets were deconstructed into individual probes and examined performance of each probe, we found that 47% of human probes were able to find their targets in canine tissues and generate a detectable hybridization signal. Therefore, we restricted gene expression analysis to these probes and observed the 60% increase in the number of identified canine transcripts. These results were validated by comparison of transcripts identified by our restricted analysis of cross-species hybridization with transcripts identified by hybridization of total lung canine mRNA to new Affymetrix Canine GeneChip(®). CONCLUSION: The experimental identification and restriction of gene expression analysis to probes with detectable hybridization signal drastically increases transcript detection of canine-human hybridization suggesting the possibility of broad utilization of cross-hybridizations of related species using GeneChip technology
Comparative Analysis of Peak Correlation Characteristics of Non-Orthogonal Spreading Codes for Wireless Systems
The performance of a CDMA based wireless system is largely dependent on the
characteristics of pseudo-random spreading codes. The spreading codes should be
carefully chosen to ensure highest possible peak value of auto-correlation
function and lower correlation peaks (side-lobes) at non-zero time-shifts.
Simultaneously, zero cross-correlation value at all time shifts is required in
order to eliminate the effect of multiple access interference at the receiver.
But no such code family exists which possess both characteristics
simultaneously. That's why an exhaustive effort has been made in this paper to
evaluate the peak correlation characteristics of various non-orthogonal
spreading codes and suggest a suitable solution.Comment: 12 Pages, 8 Figures, 3 Table
A Systematic Framework for the Construction of Optimal Complete Complementary Codes
The complete complementary code (CCC) is a sequence family with ideal
correlation sums which was proposed by Suehiro and Hatori. Numerous literatures
show its applications to direct-spread code-division multiple access (DS-CDMA)
systems for inter-channel interference (ICI)-free communication with improved
spectral efficiency. In this paper, we propose a systematic framework for the
construction of CCCs based on -shift cross-orthogonal sequence families
(-CO-SFs). We show theoretical bounds on the size of -CO-SFs and CCCs,
and give a set of four algorithms for their generation and extension. The
algorithms are optimal in the sense that the size of resulted sequence families
achieves theoretical bounds and, with the algorithms, we can construct an
optimal CCC consisting of sequences whose lengths are not only almost arbitrary
but even variable between sequence families. We also discuss the family size,
alphabet size, and lengths of constructible CCCs based on the proposed
algorithms
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