Related papers: A Compressed Self-Index for Genomic Databases
At the present scenario of the internet, there exist many optimization techniques to improve the Web speed but almost expensive in terms of bandwidth. So after a long investigation on different techniques to compress the data without any…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
Lempel-Ziv-Double (LZD) is a variation of the LZ78 compression scheme that achieves better compression on repetitive datasets. Nevertheless, prior research has identified computational inefficiencies and a weakness in its compressibility…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
This article gives a self-contained analysis of the performance of the Lempel-Ziv compression algorithm on (hidden) Markovian sources. Specifically we include a full proof of the assertion that the compression rate approaches the entropy…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
We present a simple adaptation of the Lempel Ziv 78' (LZ78) compression scheme ({\em IEEE Transactions on Information Theory, 1978}) that supports efficient random access to the input string. Namely, given query access to the compressed…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
This article introduces a new DNA sequence compression algorithm which is based on LUT and LZ77 algorithm. Combined a LUT-based pre-coding routine and LZ77 compression routine,this algorithm can approach a compression ratio of 1.9bits…
The Block Tree is a recently proposed data structure that reaches compression close to Lempel-Ziv while supporting efficient direct access to text substrings. In this paper we show how a self-index can be built on top of a Block Tree so…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
We present RCT, a new compact data structure to represent trajectories of objects. It is based on a relative compression technique called Relative Lempel-Ziv (RLZ), which compresses sequences by applying an LZ77 encoding with respect to an…
Grammar-based compression is a popular and powerful approach to compressing repetitive texts but until recently its relatively poor time-space trade-offs during real-life construction made it impractical for truly massive datasets such as…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
Compressed indexing enables powerful queries over massive and repetitive textual datasets using space proportional to the compressed input. While theoretical advances have led to highly efficient index structures, their practical…
Web archives, query and proxy logs, and so on, can all be very large and highly repetitive; and are accessed only sporadically and partially, rather than continually and holistically. This type of data is ideal for compression-based…
The well-known dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are the basis of several universal lossless compression techniques. These algorithms are asymmetric regarding encoding/decoding time and memory requirements, with…
We present a novel compressed dynamic self-index for highly repetitive text collections. Signature encoding is a compressed dynamic self-index for highly repetitive texts and has a large disadvantage that the pattern search for short…
Sequential data is being generated at an unprecedented pace in various forms, including text and genomic data. This creates the need for efficient compression mechanisms to enable better storage, transmission and processing of such data. To…
Lossless data compression has been widely studied in computer science. One of the most widely used lossless data compressions is Lempel-Zip(LZ) 77 parsing, which achieves a high compression ratio. Bidirectional (a.k.a. macro) parsing is a…