A survey on the algorithm and development of multiple sequence alignment
Multiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can
reveal the potential information in biological sequences, such as function, evolution and …
reveal the potential information in biological sequences, such as function, evolution and …
Developments in algorithms for sequence alignment: A review
J Chao, F Tang, L Xu - Biomolecules, 2022 - mdpi.com
The continuous development of sequencing technologies has enabled researchers to obtain
large amounts of biological sequence data, and this has resulted in increasing demands for …
large amounts of biological sequence data, and this has resulted in increasing demands for …
WITCH: improved multiple sequence alignment through weighted consensus hidden Markov model alignment
Accurate multiple sequence alignment is challenging on many data sets, including those
that are large, evolve under high rates of evolution, or have sequence length heterogeneity …
that are large, evolve under high rates of evolution, or have sequence length heterogeneity …
UPP2: fast and accurate alignment of datasets with fragmentary sequences
Motivation Multiple sequence alignment (MSA) is a basic step in many bioinformatics
pipelines. However, achieving highly accurate alignments on large datasets, especially …
pipelines. However, achieving highly accurate alignments on large datasets, especially …
learnMSA: learning and aligning large protein families
Background The alignment of large numbers of protein sequences is a challenging task and
its importance grows rapidly along with the size of biological datasets. State-of-the-art …
its importance grows rapidly along with the size of biological datasets. State-of-the-art …
Seqrutinator: scrutiny of large protein superfamily sequence datasets for the identification and elimination of non-functional homologues
A Amalfitano, N Stocchi, HM Atencio, F Villarreal… - Genome Biology, 2024 - Springer
Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing
and/or gene model errors and sequences from pseudogenes from complex, eukaryotic …
and/or gene model errors and sequences from pseudogenes from complex, eukaryotic …
WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity
Multiple sequence alignment is a basic part of many bioinformatics pipelines, including in
phylogeny estimation, prediction of structure for both RNAs and proteins, and metagenomic …
phylogeny estimation, prediction of structure for both RNAs and proteins, and metagenomic …
Recent progress on methods for estimating and updating large phylogenies
P Zaharias, T Warnow - Philosophical Transactions of the …, 2022 - royalsocietypublishing.org
With the increased availability of sequence data and even of fully sequenced and
assembled genomes, phylogeny estimation of very large trees (even of hundreds of …
assembled genomes, phylogeny estimation of very large trees (even of hundreds of …
UPP2: Fast and Accurate Alignment Estimation of Datasets with Fragmentary Sequences
Motivation Multiple sequence alignment (MSA) is a basic step in many bioinformatics
pipelines. However, achieving highly accurate alignments on large datasets, especially …
pipelines. However, achieving highly accurate alignments on large datasets, especially …
[PDF][PDF] DiMA: sequence diversity dynamics analyser for viruses
Sequence diversity is one of the major challenges in the design of diagnostic, prophylactic,
and therapeutic interventions against viruses. DiMA is a novel tool that is big data-ready and …
and therapeutic interventions against viruses. DiMA is a novel tool that is big data-ready and …