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Multiple protein sequence alignment and conserved domains of EnStef and stefin orthologs from selected platyhelminths and nematodes.
Here, we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments.
Wang, L.S. et al. The impact of multiple protein sequence alignment on phylogenetic estimation. in IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE Computer Society, 2009) 〈http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.68〉.org/10.1109/TCBB.2009.68〉
All currently leading protein secondary structure prediction methods use a multiple protein sequence alignment to predict the secondary structure of the top sequence.
This study is a first time attempt in using the DLT paradigm to devise efficient strategies to handle large scale multiple protein sequence alignment problem on mesh-based multiprocessor systems.
Multiple protein sequence alignments and phylogenetic trees were generated using ClustalW (align.genome.jp).jp
Multiple protein sequence alignments were performed using either the hmmalign or Muscle v3.6 [66] software.
For phylogenetic analysis, multiple protein sequence alignments were built using ClustalW [37].
For the remaining 304 clusters, multiple protein sequence alignments were generated with MUSCLE version 3.5 [60] (maximum iterations = 16).
From multiple protein sequence alignments, the A. caulinodans HyqBCEFGI hydrogenase is a constituent member of the group-4 hydrogenases.
An initial multiple sequence alignment was made using MUSCLE - multiple protein sequence alignment program in Jalview (Java alignment editor) [67], [68].
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