Families of sequences with good family complexity and cross-correlation measure

In this paper we study pseudorandomness of a family of sequences in terms of two measures, the family complexity ($f$-complexity) and the cross-correlation measure of order $\ell$. We consider sequences not only on binary alphabet but also on $k$-symbols ($k$-ary) alphabet. We first generalize some known methods on construction of the family of binary pseudorandom sequences. We prove a bound on the $f$-complexity of a large family of binary sequences of Legendre-symbols of certain irreducible polynomials. We show that this family as well as its dual family have both a large family complexity and a small cross-correlation measure up to a rather large order. Next, we present another family of binary sequences having high $f$-complexity and low cross-correlation measure. Then we extend the results to the family of sequences on $k$-symbols alphabet.Comment: 13 pages. Comments are welcome

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