منابع مشابه
Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware
With a sharp increase of available DNA and protein sequence data, new precise and fast similarity search methods are needed for largescale genome and proteome comparisons. Modern seed-based techniques of similarity search (spaced seeds, multiple seeds, subset seeds) provide a better sensitivity/specificity ratio. We present an implementation of such a seed-based technique on a parallel speciali...
متن کاملLong read alignment based on maximal exact match seeds
MOTIVATION The explosive growth of next-generation sequencing datasets poses a challenge to the mapping of reads to reference genomes in terms of alignment quality and execution speed. With the continuing progress of high-throughput sequencing technologies, read length is constantly increasing and many existing aligners are becoming inefficient as generated reads grow larger. RESULTS We prese...
متن کاملPlagiarism Alignment Detection by Merging Context Seeds
We describe our submitted algorithm to the text alignment sub-task of the plagiarism detection task in the PAN2014 challenge that achieved a plagdet score 0.855. By extracting contextual features for each document character and grouping those that are relevant for a given pair of documents, we generate seeds of atomic plagiarism cases. These are then merged by an agglomerative singlelinkage str...
متن کاملUniversal Alignment Probabilities and Subset Selection for Ordinal Optimization 1
We examine in this paper the subset selection procedure in the context of ordinal optimization introduced in [1]. Major concepts including goal softening, selection subset, alignment probability and ordered performance curve are formally introduced. A two-parameter model is devised to calculate alignment probabilities for a wide range of cases using two di erent selection rules: Blind Pick and ...
متن کاملSpaced Seeds for Cross-species Cdna-to-genome Sequence Alignment
We review recent developments in spaced seed design for cross-species sequence alignment. We start with a brief overview of original ideas and early techniques, and then focus on more recent work on finding accurate (sensitive and specific) seeds for cross-species cDNA-to-genome alignment. These recent developments include methods and models for estimating seed specificity and determining sensi...
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ژورنال
عنوان ژورنال: IEEE/ACM Transactions on Computational Biology and Bioinformatics
سال: 2009
ISSN: 1545-5963
DOI: 10.1109/tcbb.2009.4