Results 11 to 20 of about 1,261,273 (206)
Contextual Multiple Sequence Alignment [PDF]
BioMed Research International, 2005 In a recently proposed contextual alignment model, efficient algorithms exist for global and local pairwise alignment of protein sequences. Preliminary results obtained for biological data are very promising. Our main motivation was to adopt the idea of context dependency to the multiple‐alignment setting.
Rafał Otto, Anna Gambin
openaire +8 more sources
Multiple sequence alignment based on set covers [PDF]
Lecture Notes in Computer Science 3907 (2006), 127-137, 2004 We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned.
A. Bahr +15 more
arxiv +4 more sources
MAVID: Constrained ancestral alignment of multiple sequences [PDF]
arXiv, 2003 We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein based anchoring of ab-initio gene predictions, and constraints derived from a ...
Bray, Nicolas, Pachter, Lior
arxiv +7 more sources
Alignment Metric Accuracy [PDF]
arXiv, 2005 We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon previous approaches, and provides a balanced assessment of the fidelity of both matches and gaps.
Myers, Eugene W. +2 more
arxiv +4 more sources
MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments [PDF]
BMC Bioinformatics, 2012 Background The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research.
Collingridge Peter W, Kelly Steven
doaj +5 more sources
Multiple sequence alignment for short sequences [PDF]
arXiv, 2015 Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of this problem, the research on this topic is focused on aligning long sequences.
arxiv +3 more sources
Multiple sequence alignments [PDF]
Current Opinion in Structural Biology, 2005 Multiple sequence alignments are very widely used in all areas of DNA and protein sequence analysis. The main methods that are still in use are based on 'progressive alignment' and date from the mid to late 1980s. Recently, some dramatic improvements have been made to the methodology with respect either to speed and capacity to deal with large numbers ...
Desmond G. Higgins +2 more
openaire +3 more sources
Multiple Sequence Alignment Tools on the Web [PDF]
BioTechniques, 2000 The immense number of nucleotide and protein sequences that can be accessed through public databases on the Internet is an invaluable resource to scientists working in the fields of molecular biology, protein chemistry and molecular diagnostics. Tools such as BLAST (1) (also discussed in the March 2000 Internet On-Ramp) and FASTA (7) are used mainly to
Giles J. Gaskell
doaj +4 more sources
The multiple alignments of very short sequences [PDF]
FASEB BioAdvances, 2021 The multiple sequence alignment (MSA) is an increasingly important task in bioinformatics as we have to deal with the constantly increasing gene- and protein sequence databases. MSA is applied in phylogenetic analysis, in discovering conservative protein domains, in the assignment of secondary and tertiary structural features in proteins, or in the ...
Kristóf Takács, Vince Grolmusz
openaire +5 more sources
Multiple alignment by sequence annealing [PDF]
Bioinformatics, 2007 AbstractMotivation: We introduce a novel approach to multiple alignment that is based on an algorithm for rapidly checking whether single matches are consistent with a partial multiple alignment. This leads to a sequence annealing algorithm, which is an incremental method for building multiple sequence alignments one match at a time.
Schwartz, Ariel S., Pachter, Lior
openaire +4 more sources