9,919 research outputs found
EERTREE: An Efficient Data Structure for Processing Palindromes in Strings
We propose a new linear-size data structure which provides a fast access to
all palindromic substrings of a string or a set of strings. This structure
inherits some ideas from the construction of both the suffix trie and suffix
tree. Using this structure, we present simple and efficient solutions for a
number of problems involving palindromes.Comment: 21 pages, 2 figures. Accepted to IWOCA 201
PIntron: a Fast Method for Gene Structure Prediction via Maximal Pairings of a Pattern and a Text
Current computational methods for exon-intron structure prediction from a
cluster of transcript (EST, mRNA) data do not exhibit the time and space
efficiency necessary to process large clusters of over than 20,000 ESTs and
genes longer than 1Mb. Guaranteeing both accuracy and efficiency seems to be a
computational goal quite far to be achieved, since accuracy is strictly related
to exploiting the inherent redundancy of information present in a large
cluster. We propose a fast method for the problem that combines two ideas: a
novel algorithm of proved small time complexity for computing spliced
alignments of a transcript against a genome, and an efficient algorithm that
exploits the inherent redundancy of information in a cluster of transcripts to
select, among all possible factorizations of EST sequences, those allowing to
infer splice site junctions that are highly confirmed by the input data. The
EST alignment procedure is based on the construction of maximal embeddings that
are sequences obtained from paths of a graph structure, called Embedding Graph,
whose vertices are the maximal pairings of a genomic sequence T and an EST P.
The procedure runs in time linear in the size of P, T and of the output.
PIntron, the software tool implementing our methodology, is able to process in
a few seconds some critical genes that are not manageable by other gene
structure prediction tools. At the same time, PIntron exhibits high accuracy
(sensitivity and specificity) when compared with ENCODE data. Detailed
experimental data, additional results and PIntron software are available at
http://www.algolab.eu/PIntron
- …