ArticleBioinformatics (Oxford, England)2018
PASTA for proteins.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Advances in the Directed Evolution of Computer-aided Enzymes.Current topics in medicinal chemistry · 2025Review
- EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment.Algorithms for molecular biology : AMB · 2023Article
- Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires.Nucleic acids research · 2023Article
- The Studies in Constructing Yeast Cell Factories for the Production of Fatty Acid Alkyl Esters.Frontiers in bioengineering and biotechnology · 2021Review
- Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments.Database : the journal of biological databases and curation · 2020Article
- The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways.Biochemistry · 2019Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: PASTA is a multiple sequence method that uses divide-and-conquer plus iteration to enable base alignment methods to scale with high accuracy to large sequence datasets. By default, PASTA included MAFFT L-INS-i; our new extension of PASTA enables the use of MAFFT G-INS-i, MAFFT Homologs, CONTRAlign and ProbCons. We analyzed the performance of each base method and PASTA using these base methods on 224 datasets from BAliBASE 4 with at least 50 sequences. We show that PASTA enables the most accurate base methods to scale to larger datasets at reduced computational effort, and generally improves alignment and tree accuracy on the largest BAliBASE datasets. Availability and implementation: PASTA is available at https://github.com/kodicollins/pasta and has also been integrated into the original PASTA repository at https://github.com/smirarab/pasta. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.