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BMCBI
2010
198views more  BMCBI 2010»
9 years 10 months ago
ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment
Background: There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited...
Taeho Kim, Hyun Joo
BMCBI
2007
117views more  BMCBI 2007»
9 years 10 months ago
Supervised multivariate analysis of sequence groups to identify specificity determining residues
Background: Proteins that evolve from a common ancestor can change functionality over time, and it is important to be able identify residues that cause this change. In this paper ...
Iain M. Wallace, Desmond G. Higgins
BMCBI
2008
163views more  BMCBI 2008»
9 years 10 months ago
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family
Background: Multiple sequence alignments are a fundamental tool for the comparative analysis of proteins and nucleic acids. However, large data sets are no longer manageable for v...
Alberto I. Roca, Albert E. Almada, Aaron C. Abajia...
BMCBI
2010
138views more  BMCBI 2010»
9 years 10 months ago
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model
Background: While most multiple sequence alignment programs expect that all or most of their input is known to be homologous, and penalise insertions and deletions, this is not a ...
Gayathri Jayaraman, Rahul Siddharthan
BMCBI
2010
147views more  BMCBI 2010»
9 years 10 months ago
Automatic detection of anchor points for multiple sequence alignment
Background: Determining beforehand specific positions to align (anchor points) has proved valuable for the accuracy of automated multiple sequence alignment (MSA) software. This f...
Florian Pitschi, Claudine Devauchelle, Eduardo Cor...
BMCBI
2010
154views more  BMCBI 2010»
9 years 10 months ago
Fine-tuning structural RNA alignments in the twilight zone
Background: A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score ...
Andreas Bremges, Stefanie Schirmer, Robert Giegeri...
BIB
2008
86views more  BIB 2008»
9 years 10 months ago
Recent developments in the MAFFT multiple sequence alignment program
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reas...
Kazutaka Katoh, Hiroyuki Toh
ISMB
1994
9 years 11 months ago
An Efficient Method for Multiple Sequence Alignment
Multiple sequence alignment has been a useful methodin the study of molecular evolution and sequence-structure relationships. This paper presents a newmethodfor multiple sequence ...
Jin Kim, Sakti Pramanik
ISMB
1996
9 years 11 months ago
Parameterization Studies for the SAM and HMMER Methods of Hidden Markov Model Generation
Multiple sequence alignment of distantly related viral proteins remains a challenge to all currently available alignment methods. The hidden Markovmodel approach offers a new,flex...
Marcella A. McClure, Chris Smith, Pete Elton
ISMB
1996
9 years 11 months ago
The Megaprior Heuristic for Discovering Protein Sequence Patterns
Several computeralgorithms for discovering patterns in groups of protein sequences are in use that are basedon fitting the parametersof a statistical model to a group of related s...
Timothy L. Bailey, Michael Gribskov
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