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BMCBI
2005
198views more  BMCBI 2005»
13 years 3 months ago
Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural
Background: The sequencing of the human genome has enabled us to access a comprehensive list of genes (both experimental and predicted) for further analysis. While a majority of t...
Qicheng Ma, Gung-Wei Chirn, Richard Cai, Joseph D....
BMCBI
2005
132views more  BMCBI 2005»
13 years 3 months ago
Kalign - an accurate and fast multiple sequence alignment algorithm
Background: The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been applied to analyzing protein families f...
Timo Lassmann, Erik L. L. Sonnhammer
BMCBI
2005
190views more  BMCBI 2005»
13 years 3 months ago
Species-specific analysis of protein sequence motifs using mutual information
Background: Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles de...
Jan Hummel, Nima Keshvari, Wolfram Weckwerth, Joac...
BIOINFORMATICS
2005
140views more  BIOINFORMATICS 2005»
13 years 3 months ago
Profile-based direct kernels for remote homology detection and fold recognition
Motivation: Remote homology detection between protein sequences is a central problem in computational biology. Supervised learning algorithms based on support vector machines are ...
Huzefa Rangwala, George Karypis
NAR
2006
86views more  NAR 2006»
13 years 3 months ago
MODBASE: a database of annotated comparative protein structure models and associated resources
MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known p...
Ursula Pieper, Narayanan Eswar, Fred P. Davis, Han...
NAR
2006
74views more  NAR 2006»
13 years 3 months ago
HHrep: de novo protein repeat detection and the origin of TIM barrels
HHrep is a web server for the de novo identification of repeats in protein sequences, which is based on the pairwise comparison of profile hidden Markov models (HMMs). Its main st...
Johannes Söding, Michael Remmert, Andreas Bie...
NAR
2008
152views more  NAR 2008»
13 years 3 months ago
PROMALS3D web server for accurate multiple protein sequence and structure alignments
Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and ...
Jimin Pei, Ming Tang, Nick V. Grishin
IJCBDD
2008
141views more  IJCBDD 2008»
13 years 3 months ago
CLUSS2: an alignment-independent algorithm for clustering protein families with multiple biological functions
: CLUSS is an algorithm proposed for clustering both alignable and non-alignable protein sequences. However, CLUSS tends to be ineffective on protein datasets that include a large ...
Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski
BMCBI
2006
114views more  BMCBI 2006»
13 years 3 months ago
PROMPT: a protein mapping and comparison tool
Background: Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly en...
Thorsten Schmidt, Dmitrij Frishman
BMCBI
2006
143views more  BMCBI 2006»
13 years 3 months ago
IsoSVM - Distinguishing isoforms and paralogs on the protein level
Background: Recent progress in cDNA and EST sequencing is yielding a deluge of sequence data. Like database search results and proteome databases, this data gives rise to inferred...
Michael Spitzer, Stefan Lorkowski, Paul Cullen, Al...