Sentence examples for many protein alignment from inspiring English sources

Although many protein alignment methods use only local information, a few protein threading methods (Akutsu and Miyano, 1999; Godzik et al., 1992; Jones et al., 1992; Xu et al., 2003) were developed to use global information, such as pairwise contact potential, which quantifies how well two sequence residues can be placed into two template positions in a contact.

Many protein family alignments in Pfam (Finn et al., 2006), SMART (Letunic et al., 2006) and SUPERFAMILY (Wilson et al., 2007) exhibit conserved regions including blocks, or ungapped regions, within an alignment.

Frequent gaps and sequencing errors in low-quality genome assemblies were found to cause many missed protein alignments, which affected the core genome estimation.

To do so, we simulated many and varied protein alignments including coevolving residues, applied the above-mentioned methods to find these residues, and then compared their performances.

The amino acid substitution model is the core component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference.

Pfam is a large collection of multiple protein sequence alignments and Profile Hidden Markov Models covering many protein domains.

Protein sequences were aligned using ClustalW [ 23], then protein alignment was backtranslated to obtain codon alignment.

Many protein domains are very ancient.

The resulting protein alignment was reviewed and finalized using the multiple alignment sequence editor MASE.

Parsimony analyses were performed using the protein alignment as input.

As alignment cost increases in a nonlinear manner with the number of sequences, the Cons approach rapidly becomes prohibitive for larger gene families with many protein isoforms.