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» DNA Computing in Microreactors
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ISMB
1997
13 years 9 months ago
Increasing Consensus Accuracy in DNA Fragment Assemblies by Incorporating Fluorescent Trace Representations
We present a new method for determining the consensus sequence in DNA fragment assemblies. The new method, Trace-Evidence, directly incorporates aligned ABI trace information into...
Carolyn F. Allex, Schuyler F. Baldwin, Jude W. Sha...
ISMB
1996
13 years 9 months ago
Improving the Quality of Automatic DNA Sequence Assembly Using Fluorescent Trace-Data Classifications
Virtually all large-scale sequencing projects use automatic sequence-assembly programs to aid in the determination of DNA sequences. The computer-generated assemblies require subs...
Carolyn F. Allex, Schuyler F. Baldwin, Jude W. Sha...
COMPLEX
2009
Springer
13 years 9 months ago
Moving Breather Collisions in the Peyrard-Bishop DNA Model
We consider collisions of moving breathers (MBs) in the Peyrard-Bishop DNA model. Two identical stationary breathers, separated by a fixed number of pair-bases, are perturbed and b...
A. Alvarez, F. R. Romero, J. Cuevas, J. F. R. Arch...
RECOMB
2003
Springer
14 years 8 months ago
Designing seeds for similarity search in genomic DNA
Large-scale comparison of genomic DNA is of fundamental importance in annotating functional elements of genomes. To perform large comparisons efficiently, BLAST (Methods: Companio...
Jeremy Buhler, Uri Keich, Yanni Sun
RECOMB
2003
Springer
14 years 8 months ago
Modeling dependencies in protein-DNA binding sites
The availability of whole genome sequences and high-throughput genomic assays opens the door for in silico analysis of transcription regulation. This includes methods for discover...
Yoseph Barash, Gal Elidan, Nir Friedman, Tommy Kap...