9 years 5 months ago
PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination
Background: We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by ‘Pairwise Identity and Cost Scores Ordination’ (PICS-Ord)....
Robert K. Luecking, Brendan P. Hodkinson, Alexandr...
143views more  BMCBI 2010»
9 years 8 months ago
A genome alignment algorithm based on compression
Background: Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of th...
Minh Duc Cao, Trevor I. Dix, Lloyd Allison
9 years 8 months ago
Fast Smith-Waterman hardware implementation
The Smith-Waterman (SW) algorithm is one of the widely used algorithms for sequence alignment in computational biology. With the growing size of the sequence database, there is alw...
Zubair Nawaz, Koen Bertels, Huseyin Ekin Sumbul
9 years 8 months ago
TREF - TRanslation Enhancement Framework for Japanese-English
Abstract--We present a method for improving existing statistical machine translation methods using an knowledge-base compiled from a bilingual corpus as well as sequence alignment ...
Bartholomäus Wloka, Werner Winiwarter
114views more  TCBB 2010»
9 years 9 months ago
Cache-Oblivious Dynamic Programming for Bioinformatics
— We present efficient cache-oblivious algorithms for some well-studied string problems in bioinformatics including the longest common subsequence, global pairwise sequence alig...
Rezaul Alam Chowdhury, Hai-son Le, Vijaya Ramachan...
9 years 9 months ago
Network-on-Chip Hardware Accelerators for Biological Sequence Alignment
—The most pervasive compute operation carried out in almost all bioinformatics applications is pairwise sequence homology detection (or sequence alignment). Due to exponentially ...
Souradip Sarkar, Gaurav Ramesh Kulkarni, Partha Pr...
91views more  JCB 2000»
9 years 10 months ago
Scaling Laws and Similarity Detection in Sequence Alignment with Gaps
We study the problem of similarity detection by sequence alignment with gaps, using a recently established theoretical framework based on the morphology of alignment paths. Alignm...
Dirk Drasdo, Terence Hwa, Michael Lässig
156views more  BMCBI 2004»
9 years 10 months ago
DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors
Background: Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Results: Herein, a parallel version of the multi-alignment program...
Martin Schmollinger, Kay Nieselt, Michael Kaufmann...
167views more  JPDC 2007»
9 years 10 months ago
On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multiprocessor architectures
In this paper, we address the problem of multiple sequence alignment (MSA) for handling very large number of proteins sequences on mesh-based multiprocessor architectures. As the ...
Diana H. P. Low, Bharadwaj Veeravalli, David A. Ba...
158views more  BMCBI 2005»
9 years 10 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