Results 21 to 30 of about 4,572,181 (334)
A benchmark study of sequence alignment methods for protein clustering
BMC Bioinformatics, 2018 Background Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment ...
Yingying Wang, Hongyan Wu, Yunpeng Cai
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
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Briefings Bioinform., 2017 This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large ...
K. Katoh +2 more
semanticscholar +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
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Molecular biology and evolution, 2013 We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained ...
K. Katoh, D. Standley
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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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
Microbial Genomics, 2021 Command-line annotation software tools have continuously gained popularity compared to centralized online services due to the worldwide increase of sequenced bacterial genomes.
Oliver Schwengers +5 more
semanticscholar +1 more source
Accelerated large-scale multiple sequence alignment
BMC Bioinformatics, 2011 Background Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of ...
Lloyd Scott, Snell Quinn O
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Sequence‐to‐sequence alignment using a pendulum
IET Computer Vision, 2015 Analysing two or more video sequences of dynamic scenes typically requires time synchronisation between sequences, where this alignment is not always possible using hardware.
Tomislav Pribanic +2 more
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