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BMCBI
2006
117views more  BMCBI 2006»
9 years 7 months ago
Incorporating background frequency improves entropy-based residue conservation measures
Background: Several entropy-based methods have been developed for scoring sequence conservation in protein multiple sequence alignments. High scoring amino acid positions may corr...
Kai Wang, Ram Samudrala
BMCBI
2006
116views more  BMCBI 2006»
9 years 7 months ago
TaxMan: a taxonomic database manager
Background: Phylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic ...
Martin Jones, Mark Blaxter
BMCBI
2006
172views more  BMCBI 2006»
9 years 7 months ago
Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
Background: The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds ...
Jiangning Song, Kevin Burrage, Zheng Yuan, Thomas ...
BMCBI
2006
122views more  BMCBI 2006»
9 years 7 months ago
CoSMoS: Conserved Sequence Motif Search in the proteome
Background: With the ever-increasing number of gene sequences in the public databases, generating and analyzing multiple sequence alignments becomes increasingly time consuming. N...
Xiao I. Liu, Neeraj Korde, Ursula Jakob, Lars I. L...
BMCBI
2008
84views more  BMCBI 2008»
9 years 8 months ago
DNAAlignEditor: DNA alignment editor tool
Background: With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze...
Hector Sanchez-Villeda, Steven G. Schroeder, Sherr...
GECCO
2008
Springer
165views Optimization» more  GECCO 2008»
9 years 9 months ago
Multiple sequence alignment using a GLOCSA guided genetic algorithm
This paper introduces GLOCSA as a new scoring function to rate multiple sequence alignments. It is intended to be simple, considering the whole alignment at once and reflecting t...
Edgar David Arenas-Díaz, Helga Ochoterena-B...
EVOW
2010
Springer
9 years 11 months ago
Improving Multi-Relief for Detecting Specificity Residues from Multiple Sequence Alignments
A challenging problem in bioinformatics is the detection of residues that account for protein function specificity, not only in order to gain deeper insight in the nature of functi...
Elena Marchiori
BIBE
2006
IEEE
119views Bioinformatics» more  BIBE 2006»
10 years 1 months ago
Large Grain Size Stochastic Optimization Alignment
DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima pro...
Perry Ridge, Hyrum Carroll, Dan Sneddon, Mark J. C...
RECOMB
2003
Springer
10 years 8 months ago
A multi-expert system for the automatic detection of protein domains from sequence information
We describe a novel method for detecting the domain structure of a protein from sequence information alone. The method is based on analyzing multiple sequence alignments that are ...
Niranjan Nagarajan, Golan Yona
DCC
2009
IEEE
10 years 8 months ago
Source Coding Scheme for Multiple Sequence Alignments
Rapid development of DNA sequencing technologies exponentially increases the amount of publicly available genomic data. Whole genome multiple sequence alignments represent a parti...
Pavol Hanus, Janis Dingel, Georg Chalkidis, Joachi...
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