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» Alignment of Non-Overlapping Sequences
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RECOMB
2006
Springer
14 years 11 months ago
Alignment Statistics for Long-Range Correlated Genomic Sequences
It is well known that the base composition along eukaryotic genomes is long-range correlated. Here, we investigate the effect of such long-range correlations on alignment score sta...
Philipp W. Messer, Ralf Bundschuh, Martin Vingron,...
JCB
2000
105views more  JCB 2000»
13 years 10 months ago
A Greedy Algorithm for Aligning DNA Sequences
For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic progra...
Zheng Zhang 0004, Scott Schwartz, Lukas Wagner, We...
JCB
2002
116views more  JCB 2002»
13 years 10 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
BMCBI
2006
80views more  BMCBI 2006»
13 years 10 months ago
Quantification of the variation in percentage identity for protein sequence alignments
Background: Percentage Identity (PID) is frequently quoted in discussion of sequence alignments since it appears simple and easy to understand. However, although there are several...
G. P. S. Raghava, Geoffrey J. Barton
BMCBI
2005
115views more  BMCBI 2005»
13 years 10 months ago
Statistical distributions of optimal global alignment scores of random protein sequences
Background: The inference of homology from statistically significant sequence similarity is a central issue in sequence alignments. So far the statistical distribution function un...
Hongxia Pang, Jiaowei Tang, Su-Shing Chen, Shiheng...