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NAR
2011
216views Computer Vision» more  NAR 2011»
8 years 10 months ago
dbDNV: a resource of duplicated gene nucleotide variants in human genome
Gene duplications are scattered widely throughout the human genome. A single-base difference located in nearly identical duplicated segments may be misjudged as a single nucleotid...
Meng-Ru Ho, Kuo-Wang Tsai, Chun-houh Chen, Wen-cha...
CORR
2010
Springer
120views Education» more  CORR 2010»
9 years 4 months ago
Advances in the Biomedical Applications of the EELA Project
In the last years an increasing demand for Grid Infrastructures has result edin several international collaborations. This is the case of the EELA Project, which has brought togeth...
Vicente Hernández, Ignacio Blanquer, Gabrie...
NAR
2007
153views more  NAR 2007»
9 years 6 months ago
PROMALS web server for accurate multiple protein sequence alignments
Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs mu...
Jimin Pei, Bong-Hyun Kim, Ming Tang, Nick V. Grish...
JCSS
2002
95views more  JCSS 2002»
9 years 6 months ago
Efficient algorithms for locating the length-constrained heaviest segments with applications to biomolecular sequence analysis
We study two fundamental problems concerning the search for interesting regions in sequences: (i) given a sequence of real numbers of length n and an upper bound U; find a consecu...
Yaw-Ling Lin, Tao Jiang, Kun-Mao Chao
BMCBI
2005
123views more  BMCBI 2005»
9 years 7 months ago
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability
Background: Protein sequence alignments have become indispensable for virtually any evolutionary, structural or functional study involving proteins. Modern sequence search and com...
Mindaugas Margelevicius, Ceslovas Venclovas
BMCBI
2005
137views more  BMCBI 2005»
9 years 7 months ago
A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise
Background: Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topo...
Olivier Bastien, Philippe Ortet, Sylvaine Roy, Eri...
NAR
2006
128views more  NAR 2006»
9 years 7 months ago
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify cl...
Fabrice Armougom, Sébastien Moretti, Olivie...
BMCBI
2007
126views more  BMCBI 2007»
9 years 7 months ago
Multiple non-collinear TF-map alignments of promoter regions
Background: The analysis of the promoter sequence of genes with similar expression patterns is a basic tool to annotate common regulatory elements. Multiple sequence alignments ar...
Enrique Blanco, Roderic Guigó, Xavier Messe...
BMCBI
2006
111views more  BMCBI 2006»
9 years 7 months ago
Tools for integrated sequence-structure analysis with UCSF Chimera
Background: Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many pr...
Elaine C. Meng, Eric F. Pettersen, Gregory S. Couc...
BMCBI
2006
80views more  BMCBI 2006»
9 years 7 months ago
Quantification of the variation in percentage identity for protein sequence alignments
Background: Percentage Identity (PID) is frequently quoted in discussion of sequence alignments since it appears simple and easy to understand. However, although there are several...
G. P. S. Raghava, Geoffrey J. Barton
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