Searching for authors named "Jens Stoye" – sorted by Relevance.
34 documents found, showing 1 through 10.
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Algorithms for Finding Gene Clusters
- …Comparing gene orders in completely sequenced genomes is a standard approach to locate clusters of functionally associated genes.…
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Quadratic time algorithms for finding common intervals in two and more sequences
- …Abstract. A popular approach in comparative genomics is to locate groups or clusters of orthologous genes in multiple genomes and to postulate functional association between the genes contained in such clusters. To this end, genomes are often represented as permutations of their genes, and common in…
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Finding all common intervals of k permutations
- …1 Introduction Let \Pi = (ss1; : : : ; ssk) be a family of k permutations of N = f1; 2; : : : ; ng. A k-tuple of intervals of these permutations consisting of the same set of elements is called a common interval.…
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Linear Time Algorithms for Finding and Representing all Tandem Repeats in a String
- …A tandem repeat (or square) is a string ffff, where ff is a nonempty string. We present an O(jSj)-time algorithm that operates on the suffix tree T (S) for a string S, finding and marking the endpoint in T (S) of every tandem repeat that occurs in S. This decorated suffix tree implicitly represents …
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On the Similarity of Sets of Permutations and its Applications to Genome Comparison
- …The comparison of genomes with the same gene content relies on our ability to compare permutations, either by measuring how much they di#er, or by measuring how much they are alike. With the notable exception of the breakpoint distance, which is based on the concept of conserved adjacencies, meas…
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Sequence Database Search Using Jumping Alignments
- …RVKQWRAAGVPIDGIGSQTHLSAGQG d1xyza NIEDLG-PKSNA-VFN------------------MIKSMKERGVPIDGVGFQCHFINGMS d1byb GTYVTEKGKFFLTWYSN----------------KLLNHGDQILDEANKAFLGCKVKLAIK d1cnv LLSAAPGCLSPDEYLDN-----------------------AIQTRHFDYIFVRFYNDRSC d1edqa2 LMKELRAMLDQLSVETG----------------RKYELTSAISAGKDKIDKVAYNVAQNS d1…
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A Novel Approach to Remote Homology Detection: Jumping Alignments
- …We describe a new algorithm for protein classification and the detection of remote homologs. The rationale is to exploit both vertical and horizontal information of a multiple alignment in a well-balanced manner. This is in contrast to established methods such as profiles and profile hidden Markov m…
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Sequence Database Search Using Jumping Alignments
- …We describe a new algorithm for amino acid sequence classification and the detection of remote homologues. The algorithm is based on the dynamic programming principle and evaluates the fit of a candidate sequence to a given family of sequences by means of a new score called the "jumping alignment sc…
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Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment
- …The study and comparison of several sequences of characters from a finite alphabet is relevant to various areas of science, in particular molecular biology. It has been shown that multiple sequence alignment with the sum-of-pairs score is NP-hard. Recently a fast heurstic method was proposed based o…
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