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BMCBI
2007
142views more  BMCBI 2007»
13 years 7 months ago
Improving model construction of profile HMMs for remote homology detection through structural alignment
Background: Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addre...
Juliana S. Bernardes, Alberto M. R. Dávila,...
CIBCB
2005
IEEE
14 years 1 months ago
Toward Protein Structure Analysis with Self-Organizing Maps
- Establishing structure-function relationships on the proteomic scale is a unique challenge faced by bioinformatics and molecular biosciences. Large protein families represent nat...
Lutz Hamel, Gongqin Sun, Jing Zhang
BMCBI
2004
196views more  BMCBI 2004»
13 years 7 months ago
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Background: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUS...
Robert C. Edgar
BMCBI
2008
176views more  BMCBI 2008»
13 years 7 months ago
H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments
Background: A multiple sequence alignment (MSA) generated for a protein can be used to characterise residues by means of a statistical analysis of single columns. In addition to t...
Rainer Merkl, Matthias Zwick
BMCBI
2007
112views more  BMCBI 2007»
13 years 7 months ago
PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments
Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to ...
Daniel R. Caffrey, Paul H. Dana, Vidhya Mathur, Ma...