Algorithmic properties of ciliate sequence alignment

Re-Use Dynamic Programming for Sequence Alignment: An Algorithmic Toolkit

The problem of comparing two sequences S and T to determine their similarity is one of the fundamental problems in pattern matching. In this manuscript we will be primarily concerned with sequences as our objects and with various string comparison metrics. Our goal is to survey a methodology for utilizing repetitions in sequences in order to speed up the comparison process. Within this framewor...

ALGORITHMIC PROPERTIES OF AUTARKIES Algorithmic properties of autarkies

Autarkies arise in studies of satisfiability of CNF theories. In this paper we extend the notion of an autarky to arbitrary propositional theories. We note that in this general setting autarkies are related to the 3-valued logic. Most of our results are concerned with algorithmic properties of autarkies. We prove that the problem of the existence of autarkies is NP-complete and that, as in the ...

Multiple Sequence Alignment Multiple Sequence Alignment

An algorithm for progressive multiple alignment of sequences with insertions " , 1. Introduction The problem of sequence alignment is to find the patterns of sequence conservation and similarity between pairs or sets of given sequences. In biological contexts, similarity between biological sequences usually amounts to either functional or structural similarities or divergence from a common ance...

Some Properties of Ciliate Bio-operations

The process of gene unscrambling in ciliates (a type of unicellular protozoa), which accomplishes the difficult task of re-arranging gene segments in the correct order and deleting non-coding sequences from an “encrypted” version of a DNA strand, has been modeled and studied so far from the point of view of the computational power of the DNA bio-operations involved. Here we concentrate on a dif...

Sequence Alignment