On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given pattern of length $m$ in $O(\frac{m}{p}+ \lg p + \lg\lg p\cdot\lg\lg n)$ time for $p \le m$. For approximate pattern matching with $k$ differences or mismatches, we show how to compute all occurrences of a given pattern in $O(\frac{m^k\sigma^k}{p}\max\left(k,\lg\lg n\right)\!+\!(1+\frac{m}{p}) \lg p\cdot \lg\lg n + \text{occ})$ time, where $\sigma$ is the size of the alphabet and $p \le \sigma^k m^k$. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns $P$ and $P'$, we present a data structure for computing the interval of $PP'$ in $O(\lg\lg n)$ sequential time, or in $O(1+\lg_p\lg n)$ parallel time. All our data structures are of size $O(n)$ bits (in addition to the suffix array)

Succinct Representations of Dynamic Strings

The rank and select operations over a string of length n from an alphabet of size $\sigma$ have been used widely in the design of succinct data structures. In many applications, the string itself need be maintained dynamically, allowing characters of the string to be inserted and deleted. Under the word RAM model with word size $w=\Omega(\lg n)$, we design a succinct representation of dynamic strings using $nH_0 + o(n)\lg\sigma + O(w)$ bits to support rank, select, insert and delete in $O(\frac{\lg n}{\lg\lg n}(\frac{\lg \sigma}{\lg\lg n}+1))$ time. When the alphabet size is small, i.e. when \sigma = O(\polylog (n)), including the case in which the string is a bit vector, these operations are supported in $O(\frac{\lg n}{\lg\lg n})$ time. Our data structures are more efficient than previous results on the same problem, and we have applied them to improve results on the design and construction of space-efficient text indexes

A simple and optimal ancestry labeling scheme for trees

We present a $\lg n + 2 \lg \lg n+3$ ancestry labeling scheme for trees. The problem was first presented by Kannan et al. [STOC 88'] along with a simple $2 \lg n$ solution. Motivated by applications to XML files, the label size was improved incrementally over the course of more than 20 years by a series of papers. The last, due to Fraigniaud and Korman [STOC 10'], presented an asymptotically optimal $\lg n + 4 \lg \lg n+O(1)$ labeling scheme using non-trivial tree-decomposition techniques. By providing a framework generalizing interval based labeling schemes, we obtain a simple, yet asymptotically optimal solution to the problem. Furthermore, our labeling scheme is attained by a small modification of the original $2 \lg n$ solution.Comment: 12 pages, 1 figure. To appear at ICALP'1

Milk whey protein concentration and mRNA associated with β-lactoglobulin phenotype

Two common genetic variants of β-lactoglobulin (β-lg), A and B, exist as co- dominant alleles in dairy cattle (Aschaffenburg, 1968). Numerous studies have shown that cows homozygous for β-lg A have more β-lg and less α-lactalbumin (α-la) and casein in their milk than cows expressing only the B variant of β-lg (Ng-Kwai-Hang et al. 1987; Graml et al. 1989; Hill, 1993; Hill et al. 1995, 1997). These differences have a significant impact on the processing characteristics of the milk. For instance, the moisture-adjusted yield of Cheddar cheese is up to 10% higher using milk from cows of the β-lg BB phenotype compared with milk from cows expressing only the A variant (Hill et al. 1997). All these studies, however, describe compositional differences associated with β-lg phenotype in established lactation only. No information is available on the first few weeks of lactation, when there are marked changes in the concentrations of β-lg and α-la (Pérez et al. 1990)