Sentence examples for alignment via the from inspiring English sources

The protein sequences were aligned using multiple sequence alignment via the ClustalW method and were then manually corrected and implemented in the MEGA4 software (version 4.0) [ 89].

Using the program YN00 from the PAML package [ 32] we estimated synonymous (dS) and non-synonymous (dN) substitution rates for each alignment via the method of Yang and Nielsen [ 33].

The pipeline procedure aligns reads by barcode type, trims barcodes off to give sequences of 64 bp, merges tag files of the same individual (default minimum number of times a tag must be present to be output = 5), gives pairwise alignment via the network filter (ETR = 0.03), and assigns genotypes to each individual (allele frequency minimum = 0.05; maximum = 0.5).

Then, to validate the relevance of the other 4 domain hits, structural alignments (via the jCE algorithm [ 34]) were executed for each representative PDB structure of the domains against the PDB structure 1YMG|A.

Furthermore, to clarify if Q9K8K1_BACHD can be generalized as a sugar transporter, the PDB structure 2CFP|A was used as a surrogate structure to Q9K8K1_BACHD for performing structural alignments (via the jCE algorithm [ 34]) against the representative PDB structures (if available) of the domain hits in Table  4.

Transcriptional start sites were first determined in D. melanogaster using experimental data collected in the Eukaryotic Promoter Database [73] and extrapolated to other species by referencing the whole genome alignments via the UCSC Genome Browser (http://genome.ucsc.edu/).ucsc.edu/

The assembly of alignments via the PASA alignment assembly algorithm, and subsequent clustering of overlapping alignment assemblies with same transcribed orientation were performed exactly as previously described.

Enoplid sequences generated during this investigation were incorporated into nematode secondary structure alignments via the Positional Tree (PT) Server function in the ARB software suite.

Individual gene trees were tested for compatibility against the concatenated alignments via the approximately unbiased (AU) test as employed in Consel (Shimodaira 2002).

Values of the measures of similarity (2.4) of algorithmic alignments via the reference alignments derived from "native" matrix and the PAM250 matrix, are practically the same (difference less than 1%, see the table in additional file 1, sheet PAM250).

A specific interface has been developed to perform various operations such as the intersection or the difference between two gene carts, to extract sequences or to run multiple alignments via the plugged Jalview software (36).