Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA forensics. However, real-world DNA sequences may comprise several Gigabytes and the process of DNA analysis demands adequate computational resources to be completed within a reasonable time. In this paper we present a scalable approach for parallel DNA analysis that is based on Finite Automata, and which is suitable for analyzing very large DNA segments. We evaluate our approach for real-world DNA segments of mouse (2.7GB), cat (2.4GB), dog (2.4GB), chicken (1GB), human (3.2GB) and turkey (0.2GB). Experimental results on a dual-socket shared-memory system with 24 physical cores show speed-ups of up to 17.6x. Our approach is up to 3x faster than a pattern-based parallel approach that uses the RE2 library.
Mar c ais and Kingsford @cite_30 present the Jellyfish tool, which is based on the lock-free hash table that is optimized for counting @math -mers of length up to 31 bases. @cite_18 present a similar approach to Jellyfish @cite_30 , so called DSK, which is designed for small-memory servers. The @math -mers are counted by traversing the hash tables. Using hash tables for the internal representation resulted to be memory inefficient @cite_20 . As described by @cite_20 a sequence corresponding to a human chromosome with 24-230MB of input data would require gigabytes of memory to store the @math -mers information.
@cite_30 @cite_18 @cite_20
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Motivation: Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm. Results: We propose a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient. It is based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length. Due to their flexibility, suffix arrays have been the data structure of choice for solving many string problems. For the task of k-mer counting, important in many biological applications, Jellyfish offers a much faster and more memory-efficient solution. Availability: The Jellyfish software is written in C++ and is GPL licensed. It is available for download at http: www.cbcb.umd.edu software jellyfish. Contact: [email protected] Supplementary information:Supplementary data are available at Bioinformatics online. Summary: Counting all the k-mers (substrings of length k )i n DNA RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory. Such structure typically grows with the number of distinct k -mers to count. We present an ew streaming algorithm for k-mer counting, called DSK (disk streaming of k-mers), which only requires a fixed user-defined amount of memory and disk space. This approach realizes a memory, time and disk trade-off. The multi-set of all k-mers present in the reads is partitioned, and partitions are saved to disk. Then, each partition is separately loaded in memory in a temporary hash table. The k-mer counts are returned by traversing each hash table. Low-abundance k-mers are optionally filtered. DSK is the first approach that is able to count all the 27-mers of a human genome dataset using only 4.0 GB of memory and moderate disk space (160 GB), in 17.9 h. DSK can replace a popular k-mer counting software (Jellyfish) on small-memory servers. Availability: http: minia.genouest.org dsk Contact: rayan.chikhi@ens-cachan.org Given a sequence S e s1s2…sn of integers smaller than r e O(polylog(n)), we show how S can be represented using nH0(S) p o(n) bits, so that we can know any sq, as well as answer rank and select queries on S, in constant time. H0(S) is the zero-order empirical entropy of S and nH0(S) provides an information-theoretic lower bound to the bit storage of any sequence S via a fixed encoding of its symbols. This extends previous results on binary sequences, and improves previous results on general sequences where those queries are answered in O(log r) time. For larger r, we can still represent S in nH0(S) p o(n log r) bits and answer queries in O(log r log log n) time. Another contribution of this article is to show how to combine our compressed representation of integer sequences with a compression boosting technique to design compressed full-text indexes that scale well with the size of the input alphabet Σ. Specifically, we design a variant of the FM-index that indexes a string T[1, n] within nHk(T) p o(n) bits of storage, where Hk(T) is the kth-order empirical entropy of T. This space bound holds simultaneously for all k ≤ α logvΣv n, constant 0 Compared to all previous works, our index is the first that removes the alphabet-size dependance from all query times, in particular, counting time is linear in the pattern length. Still, our index uses essentially the same space of the kth-order entropy of the text T, which is the best space obtained in previous work. We can also handle larger alphabets of size vΣv e O(nβ), for any 0 This paper presents a family of bitmap algorithms that address the problem of counting the number of distinct header patterns (flows) seen on a high-speed link. Such counting can be used to detect DoS attacks and port scans and to solve measurement problems. Counting is especially hard when processing must be done within a packet arrival time (8 ns at OC-768 speeds) and, hence, may perform only a small number of accesses to limited, fast memory. A naive solution that maintains a hash table requires several megabytes because the number of flows can be above a million. By contrast, our new probabilistic algorithms use little memory and are fast. The reduction in memory is particularly important for applications that run multiple concurrent counting instances. For example, we replaced the port-scan detection component of the popular intrusion detection system Snort with one of our new algorithms. This reduced memory usage on a ten minute trace from 50 to 5.6 MB while maintaining a 99.77 probability of alarming on a scan within 6 s of when the large-memory algorithm would. The best known prior algorithm (probabilistic counting) takes four times more memory on port scan detection and eight times more on a measurement application. This is possible because our algorithms can be customized to take advantage of special features such as a large number of instances that have very small counts or prior knowledge of the likely range of the count.