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» Efficient protein alignment algorithm for protein search
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BMCBI
2005
119views more  BMCBI 2005»
13 years 5 months ago
The distance-profile representation and its application to detection of distantly related protein families
Background: Detecting homology between remotely related protein families is an important problem in computational biology since the biological properties of uncharacterized protei...
Chin-Jen Ku, Golan Yona
ISMB
1997
13 years 6 months ago
Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations
The structural comparison of proteins has become increasingly important as a means to identify protein motifs and fold families. In this paper we present a new algorithm for the c...
Amit Pal Singh, Douglas L. Brutlag
BMCBI
2011
12 years 9 months ago
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs
Background: Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for seque...
Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzy...
BMCBI
2010
137views more  BMCBI 2010»
13 years 5 months ago
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
Background: While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor ...
Michael L. Sierk, Michael E. Smoot, Ellen J. Bass,...
BMCBI
2007
149views more  BMCBI 2007»
13 years 5 months ago
SAMPI: Protein Identification with Mass Spectra Alignments
Background: Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by tryps...
Hans-Michael Kaltenbach, Andreas Wilke, Sebastian ...