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» A Part-of-Speech-Based Alignment Algorithm
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NAACL
2004
15 years 5 months ago
What's in a translation rule?
We propose a theory that gives formal semantics to word-level alignments defined over parallel corpora. We use our theory to introduce a linear algorithm that can be used to deriv...
Michel Galley, Mark Hopkins, Kevin Knight, Daniel ...
RECOMB
2005
Springer
16 years 4 months ago
Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution
Abstract. With ever increasing amount of available data on protein-protein interaction (PPI) networks and research revealing that these networks evolve at a modular level, discover...
Mehmet Koyutürk, Ananth Grama, Wojciech Szpan...
135
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BMCBI
2008
103views more  BMCBI 2008»
15 years 4 months ago
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model
Background: Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have ...
Mallika Veeramalai, Yuzhen Ye, Adam Godzik
RECOMB
2008
Springer
16 years 4 months ago
A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery
As an increasing number of eukaryotic genomes are being sequenced, comparative studies aimed at detecting regulatory elements in intergenic sequences are becoming more prevalent. M...
Raluca Gordân, Leelavati Narlikar, Alexander...
RECOMB
2006
Springer
16 years 4 months ago
Structural Alignment of Pseudoknotted RNA
In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseu...
Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna