Sentence examples for 1 alignments from inspiring English sources

Fig. 1 Alignments of mtDNA ND5 and cytb gene from cat, human, dog, pig, cattle, sheep, goat, horse, goose, chicken, and duck.

1) Alignments and Phylogenetic Inference, last sentence: It is not clear what "cf" stands for.

Both background and procedures of the phylogenetic analysis are described in Additional File 1, alignments are shown in Additional Files 2, 3, 4 and 5, calculations of sequence identities are given in Additional Files 6 and 7, and phylogenetic trees are shown in Additional Files 8, 9, 10, 11 and 12.

For TBLASTN, alignments are divided into three categories: (1) alignments that match a query to the coding region of a known true positive match; (2) alignments that match a query to a known coding region that is not a true positive match; and (3) alignments that do not match a known coding region.

Fig. 1 Alignment plot of Nostoc punctiforme ATCC 29133 genomes.

This study also presents a large scale comparison between 10 methods—9 alignment-free and 1 alignment-based.

Additional file 1: Alignment of LRX3, LRX4 and LRX5 proteins.

In the final datasets there were a total of 369 nucleotide positions in PT HIV-2 and 372 positions in PT HIV-1 alignments, and 369 positions in HIV-2 and HIV-1 Control alignments.

We developed a maximum likelihood model fitting procedure to a collection of HIV-1 alignments sampled from different viral genes, and inferred two empirical substitution models, suitable for describing between-and within-host evolution.

ECM is ranked second when fitted to one of the alignments used in ECM estimation (PF00803), yet fits rhodopsin and HIV-1 alignments worse than the single rate model, suggesting it may be impossible to derive a generalist empirical codon model.

Our models had a consistently superior fit relative to the best existing models and to parameter-rich data-driven models when benchmarked on independent HIV-1 alignments, demonstrating evolutionary biases in amino-acid substitution that are unique to HIV, and that are not captured by the existing models.