libFLASM: a software library for fixed-length approximate string matching
نویسندگان
چکیده
منابع مشابه
A Parallel Algorithm for the Fixed-length Approximate String Matching Problem for High Throughput Sequencing Technologies
The approximate string matching problem is to find all locations at which a query of length m matches a substring of a text of length n with k-or-fewer differences. Nowadays, with the advent of novel high throughput sequencing technologies, the approximate string matching algorithms are used to identify similarities, molecular functions and abnormalities in DNA sequences. We consider a generali...
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This paper deals with the approximate string-matching problem with Hamming distance. The approximate string-matching with kmismatches problem is to find all locations at which a query of length m matches a factor of a text of length n with k or fewer mismatches. The approximate string-matching algorithms have both pleasing theoretical features, as well as direct applications, especially in comp...
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Searching for DNA or amino acid sequences similar to a given pattern string is very important in molecular biology. In fact, a lot of programs and algorithms have been developed. Most of them are based on alignment of strings or approximate string matching. However, they do not seem to be adequate in some cases. For example, the DNA pattern TATA (known as TATA box) is a common promoter that oft...
متن کاملA Metric Index for Approximate String Matching
We present a radically new indexing approach for approximate string matching. The scheme uses the metric properties of the edit distance and can be applied to any other metric between strings. We build a metric space where the sites are the nodes of the suffix tree of the text, and the approximate query is seen as a proximity query on that metric space. This permits us finding the occ occurrenc...
متن کاملA Faster Algorithm for Approximate String Matching
We present a new algorithm for on line approximate string matching The algorithm is based on the simulation of a non deterministic nite automaton built from the pattern and using the text as input This simulation uses bit operations on a RAM machine with word length O log n being n the maximum size of the text The running time achieved is O n for small patterns i e m O p log n independently of ...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2016
ISSN: 1471-2105
DOI: 10.1186/s12859-016-1320-2