Results 21 to 30 of about 4,504,319 (408)
Using structure to explore the sequence alignment space of remote homologs. [PDF]
PLoS Computational Biology, 2011 Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate ...
Andrew Kuziemko +2 more
doaj +1 more source
Spark-based Parallelization of Basic Local Alignment Search Tool [PDF]
International Journal Bioautomation, 2020 Sequence alignment is a key link of bioinformatics analysis. The basic local alignment search tool (BLAST) is a popular sequence alignment algorithm with high accuracy. However, the BLAST is inefficient in comparing and analyzing a massive amount of gene
Hui Wang +4 more
doaj +1 more source
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. [PDF]
, 2006 BackgroundOne of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models.
Bourne, Philip E, Scheeff, Eric D
core +3 more sources
The Sequence Alignment/Map format and SAMtools
Bioinform., 2009 Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.
Heng Li +8 more
semanticscholar +1 more source
Current Trends and Ongoing Progress in the Computational Alignment of Biological Sequences
IEEE Access, 2019 The computational techniques for nucleic acid and protein sequence comparison reduce the extensive burden of molecular biologists. The sequence alignment is one of the main research areas in bioinformatics, and comparative genomics and proteomics lead us
Muhammad Ishaq +3 more
doaj +1 more source
Nucleic Acids Research, 1994 The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences.
J. Thompson, D. Higgins, T. Gibson
semanticscholar +1 more source
Nucleic Acids Research, 1997 CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the ...
J. Thompson +4 more
semanticscholar +1 more source
bioRxiv, 2021 Multiple sequence alignments are widely used to infer evolutionary relationships, enabling inferences of structure, function, and phylogeny. Standard practice is to construct one alignment by some preferred method and use it in further analysis; however,
Robert C. Edgar
semanticscholar +1 more source
An enhanced RNA alignment benchmark for sequence alignment programs
Algorithms for Molecular Biology, 2006 Background The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for the RNA alignment problem, as was ...
Steger Gerhard +2 more
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MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Nucleic Acids Research, 2004 We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log ...
Robert C. Edgar
semanticscholar +1 more source