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» A Part-of-Speech-Based Alignment Algorithm
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JCB
2002
116views more  JCB 2002»
15 years 3 months ago
A Novel Approach to Remote Homology Detection: Jumping Alignments
We describe a new algorithm for protein classi cation and the detection of remote homologs. The rationale is to exploit both vertical and horizontal information of a multiple alig...
Rainer Spang, Marc Rehmsmeier, Jens Stoye
IICAI
2007
15 years 5 months ago
A Java Implementation of an Extended Word Alignment Algorithm Based on the IBM Models
In recent years statistical word alignment models have been widely used for various Natural Language Processing (NLP) problems. In this paper we describe a platform independent and...
G. Chinnappa, Anil Kumar Singh
GECCO
2003
Springer
128views Optimization» more  GECCO 2003»
15 years 9 months ago
Evolving Consensus Sequence for Multiple Sequence Alignment with a Genetic Algorithm
In this paper we present an approach that evolves the consensus sequence [25] for multiple sequence alignment (MSA) with genetic algorithm (GA). We have developed an encoding schem...
Conrad Shyu, James A. Foster
RECOMB
2009
Springer
16 years 4 months ago
Lifting Prediction to Alignment of RNA Pseudoknots
Prediction and alignment of RNA pseudoknot structures are NP-hard. Nevertheless, several efficient prediction algorithms by dynamic programming have been proposed for restricted cl...
Mathias Möhl, Rolf Backofen, Sebastian Will
BMCBI
2005
158views more  BMCBI 2005»
15 years 3 months ago
Automated generation of heuristics for biological sequence comparison
Background: Exhaustive methods of sequence alignment are accurate but slow, whereas heuristic approaches run quickly, but their complexity makes them more difficult to implement. ...
Guy St. C. Slater, Ewan Birney