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236views Computer Vision» more  NAR 2011»
10 years 2 months ago
The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish
The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalu...
Jianguo Lu, Eric Peatman, Qing Yang, Shaolin Wang,...
10 years 6 months ago
RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
Background: Computational analysis of metagenomes requires the taxonomical assignment of the genome contigs assembled from DNA reads of environmental samples. Because of the diver...
Ozkan U. Nalbantoglu, Samuel F. Way, Steven H. Hin...
123views more  NAR 2000»
10 years 11 months ago
The Protein Information Resource (PIR)
The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIRInternational Protein Sequence Da...
Winona C. Barker, John S. Garavelli, Hongzhan Huan...
124views more  BMCBI 2005»
10 years 11 months ago
Probabilistic annotation of protein sequences based on functional classifications
: One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. ...
Emmanuel D. Levy, Christos A. Ouzounis, Walter R. ...
75views more  JCB 2008»
10 years 11 months ago
New, Improved, and Practical k-Stem Sequence Similarity Measures for Probe Design
We define new measures of sequence similarity for oligonucleotide probe design. These new measures incorporate the nearest neighbor k-stem motifs in their definition, but can be e...
Anthony J. Macula, Alexander Schliep, Morgan A. Bi...
157views Education» more  CORR 2010»
10 years 11 months ago
Efficient Clustering with Limited Distance Information
Given a point set S and an unknown metric d on S, we study the problem of efficiently partitioning S into k clusters while querying few distances between the points. In our model ...
Konstantin Voevodski, Maria-Florina Balcan, Heiko ...
158views more  BMCBI 2008»
10 years 11 months ago
Metrics for GO based protein semantic similarity: a systematic evaluation
Background: Several semantic similarity measures have been applied to gene products annotated with Gene Ontology terms, providing a basis for their functional comparison. However,...
Catia Pesquita, Daniel Faria, Hugo P. Bastos, Ant&...
189views more  BMCBI 2010»
10 years 11 months ago
High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH
Background: Protein alignments are an essential tool for many bioinformatics analyses. While sequence alignments are accurate for proteins of high sequence similarity, they become...
Florian Teichert, Jonas Minning, Ugo Bastolla, Mar...
150views more  BMCBI 2010»
10 years 11 months ago
Evolutionary rates at codon sites may be used to align sequences and infer protein domain function
Background: Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structu...
Pierre M. Durand, Scott Hazelhurst, Theresa L. Coe...
11 years 24 days ago
Modeling sequence and function similarity between proteins for protein functional annotation
A common task in biological research is to predict function for proteins by comparing sequences between proteins of known and unknown function. This is often done using pair-wise ...
Roger Higdon, Brenton Louie, Eugene Kolker