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» Efficient protein alignment algorithm for protein search
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BMCBI
2007
105views more  BMCBI 2007»
15 years 6 months ago
Generating confidence intervals on biological networks
Background: In the analysis of networks we frequently require the statistical significance of some network statistic, such as measures of similarity for the properties of interact...
Thomas Thorne, Michael P. H. Stumpf
BMCBI
2006
117views more  BMCBI 2006»
15 years 6 months ago
Gene Designer: a synthetic biology tool for constructing artificial DNA segments
Background: Direct synthesis of genes is rapidly becoming the most efficient way to make functional genetic constructs and enables applications such as codon optimization, RNAi re...
Alan Villalobos, Jon E. Ness, Claes Gustafsson, Je...
BIBE
2003
IEEE
183views Bioinformatics» more  BIBE 2003»
15 years 11 months ago
Effective Indexing and Filtering for Similarity Search in Large Biosequence Databases
We present a multi-dimensional indexing approach for fast sequence similarity search in DNA and protein databases. In particular, we propose effective transformations of subsequen...
Ozgur Ozturk, Hakan Ferhatosmanoglu
CSB
2004
IEEE
142views Bioinformatics» more  CSB 2004»
15 years 9 months ago
FastR: Fast Database Search Tool for Non-Coding RNA
The discovery of novel non-coding RNAs has been among the most exciting recent developments in Biology. Yet, many more remain undiscovered. It has been hypothesized that there is ...
Vineet Bafna, Shaojie Zhang
RECOMB
1998
Springer
15 years 10 months ago
Alignments without low-scoring regions
Given a strong match between regions of two sequences, how far can the match be meaningfully extended if gaps are allowed in the resulting alignment? The aim is to avoid searching...
Zheng Zhang 0004, Piotr Berman, Webb Miller