Related papers: Reusing an FM-index
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
The FM-index is a celebrated compressed data structure for full-text pattern searching. After the first wave of interest in its theoretical developments, we can observe a surge of interest in practical FM-index variants in the last few…
We consider how to index strings, trees and graphs for jumbled pattern matching when we are asked to return a match if one exists. For example, we show how, given a tree containing two colours, we can build a quadratic-space index with…
We consider strategies to organize easily updatable associative arrays in external memory. These arrays are used for full-text search. We study indexes with different keys: single word form, two word forms, and sequences of word forms. The…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…
Similarity searching finds application in a wide variety of domains including multilingual databases, computational biology, pattern recognition and text retrieval. Similarity is measured in terms of a distance function, edit distance, in…
Searches for phrases and word sets in large text arrays by means of additional indexes are considered. Their use may reduce the query-processing time by an order of magnitude in comparison with standard inverted files.
Suppose we have just performed searches in a self-index for two patterns $A$ and $B$ and now we want to search for their concatenation \A B); how can we best make use of our previous computations? In this paper we consider this problem and,…
Previous authors have shown how to build FM-indexes efficiently in external memory, but querying them efficiently remains an open problem. Searching na\"{i}vely for a pattern $P$ requires (\Theta (|P|)) random access. In this paper we show…
Let S be a finite, ordered alphabet, and let x = x_1 x_2 ... x_n be a string over S. A "secondary index" for x answers alphabet range queries of the form: Given a range [a_l,a_r] over S, return the set I_{[a_l;a_r]} = {i |x_i \in [a_l;…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…
Applications in domains ranging from bioinformatics to advertising feature strings that come with numerical scores (utilities). The utilities quantify the importance, interest, profit, or risk of the letters occurring at every position of a…
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…
Associative memories are data structures that allow retrieval of stored messages from part of their content. They thus behave similarly to human brain that is capable for instance of retrieving the end of a song given its beginning. Among…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
We propose an improvement of the known DFT-based indexing technique for fast retrieval of similar time sequences. We use the last few Fourier coefficients in the distance computation without storing them in the index since every coefficient…