A compressed text database based on the compressed suffix array is proposed. The compressed su#x array of Grossi and Vitter occupies only O(n) bits for a text of length n; however it also uses the text itself that occupies O(n log bits for the alphabet #. On the other hand, our data structure does not use the text itself, and supports important operations for text databases: inverse, search and decompress. Our algorithms can find occ occurrences of any substring P of the text

this paper we show experimentally that, for large or small collections, storing integers in a compressed format reduces the time required for either sequential stream access or random access. We compare di#erent approaches to compressing integers, including the Elias gamma and delta codes, Golomb coding, and a variable-byte integer scheme. As a conclusion, we recommend that, for fast access to integers, files be stored compressed

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. Inverted index compression, block addressing and sequential search on compressed text are three techniques that have been separately developed for efficient, low-overhead text retrieval. Modern text compression techniques can reduce the text to less than 30% of its size and allow searching it directly and faster than the uncompressed text. Inverted index compression obtains significant reduction of their original size at the same processing speed. Block addressing makes the inverted lists point to text blocks instead of exact positions and pay the reduction in space with some sequential text scanning. In this work we combine the three ideas in a single scheme. We present a compressed inverted file that indexes compressed text and uses block addressing. We consider different techniques to compress the index and study their performance with respect to the block size. We compare the index against three separate techniques for varying block sizes, showing that our index is superior to each isolated approach. For instance, with just 4% of extra space overhead the index has to scan less than 12% of the text for exact searches and about 20% allowing one error in the matches. Keywords: Text compression, inverted files, block addressing, text databases. 1.

The classical algorithm for computing the similarity between two sequences [36, 39] uses a dynamic programming matrix, and compares two strings of size n in O(n 2 ) time. We address the challenge of computing the similarity of two strings in sub-quadratic time, for metrics which use a scoring matrix of unrestricted weights. Our algorithm applies to both local and global alignment computations. The speed-up is achieved by dividing the dynamic programming matrix into variable sized blocks, as induced by Lempel-Ziv parsing of both strings, and utilizing the inherent periodic nature of both strings. This leads to an O(n 2 = log n) algorithm for an input of constant alphabet size. For most texts, the time complexity is actually O(hn 2 = log n) where h 1 is the entropy of the text. Institut Gaspard-Monge, Universite de Marne-la-Vallee, Cite Descartes, Champs-surMarne, 77454 Marne-la-Vallee Cedex 2, France, email: mac@univ-mlv.fr. y Department of Computer Science, Haifa University, Haifa 31905, Israel, phone: (972-4) 824-0103, FAX: (972-4) 824-9331; Department of Computer and Information Science, Polytechnic University, Six MetroTech Center, Brooklyn, NY 11201-3840; email: landau@poly.edu; partially supported by NSF grant CCR-0104307, by NATO Science Programme grant PST.CLG.977017, by the Israel Science Foundation (grants 173/98 and 282/01), by the FIRST Foundation of the Israel Academy of Science and Humanities, and by IBM Faculty Partnership Award. z Department of Computer Science, Haifa University, Haifa 31905, Israel; On Education Leave from the IBM T.J.W. Research Center; email: michal@cs.haifa.il; partially supported by by the Israel Science Foundation (grants 173/98 and 282/01), and by the FIRST Foundation of the Israel Academy of Science ...

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. We consider the problem of coding planar graphs by binary strings. Depending on whether O(1)-time queries for adjacency and degree are supported, we present three sets of coding schemes which all take linear time for encoding and decoding. The encoding lengths are significantly shorter than the previously known results in each case. 1 Introduction This paper investigates the problem of encoding a graph G with n nodes and m edges into a binary string S. This problem has been extensively studied with three objectives: (1) minimizing the length of S, (2) minimizing the time needed to compute and decode S, and (3) supporting queries efficiently. A number of coding schemes with different trade-offs have been proposed. The adjacency-list encoding of a graph is widely useful but requires 2mdlog ne bits. (All logarithms are of base 2.) A folklore scheme uses 2n bits to encode a rooted n-node tree into a string of n pairs of balanced parentheses. Since the total number of such trees is...

Genomic sequence databases are widely used by molecular biologists for homology searching. Amino-acid and nucleotide databases are increasing in size exponentially, and mean sequence lengths are also increasing. In searching such databases, it is desirable to use heuristics to perform computationally intensive local alignments on selected sequences only and to reduce the costs of the alignments that are attempted. We present an index-based approach for both selecting sequences that display broad similarity to a query and for fast local alignment. We show experimentally that the indexed approach results in signi cant savings in computationally intensive local alignments, and that index-based searching is as accurate as existing exhaustive search schemes.

We discuss space-efficient encoding schemes for planar graphs and maps. Our results improve on the constants of previous schemes and can be achieved with simple encoding algorithms. They are near-optimal in number of bits per edge. 1 Introduction In this paper we discuss space-efficient binary encoding schemes for several classes of unlabeled connected planar graphs and maps. In encoding a graph we must encode the incidences among vertexes and edges. By maps we understand topological equivalence classes of planar embeddings of planar graphs. In encoding a map we are required to encode the topology of the embedding i.e., incidences among faces, edges, and vertexes, as well as the graph. Each map is an embedding of a unique graph, but a given graph may have multiple embeddings. Hence maps must require more bits to encode than graphs in some average sense. There are a number of recent results on space-efficient encoding. A standard adjacency list encoding of an unlabeled graph G requires...