Sentence examples for by generating an alignment from inspiring English sources

We further investigated the relationship between the Arabidopsis and rice IQD protein families by generating an alignment of the 61 identified IQD amino acid sequences followed by the generation of a neighbor-joining phylogenetic tree.

We further investigated the relationship between the Arabidopsis and rice PP2C protein families by generating an alignment of the full-length protein sequences of 78 OsPP2Cs and 80 AtPP2Cs followed by the construction of a phylogenetic tree.

The phylogenetic relationships between the human (Homo sapiens), zebrafish, mouse (Mus musculus), chicken (Gallus gallus) and coelacanth (Latimeria chalumnae) genes encoding the APOA-I, APOB, APOE and APOA-IV proteins were examined by generating a multiple sequence alignment with the iterative MAFFT multiple alignment tool.

Coverage of the genome sequence by RNA-seq transcripts was determined by generating a "base pair map" of the.bam alignment using the bam2depth function in SAMtools (http://samtools.sourceforge.net) [ 42].

Since EC3 loop contains a motif similar to ion channel selectivity filter, we generated an alignment guided by presence of similar motifs to generate Model 3 (using alignment in Fig. S2C).

We performed a series of simulations by generating alignments of 1000, 2000, and 10,000 nt in length with a tree similar to the influenza A virus data set and with a rate shift in the centre of the tree.

To more thoroughly examine evolutionary patterns and modes of sequence evolution within each of these Hsp70 subfamilies, we analyzed them individually by generating separate sequence alignments for each.

This optimization was carried out by generating all possible ungapped alignments, for which a score is assigned according to the quality of their corresponding models.

To further characterize the hemagglutinin gene from the Fraser Valley HPAI isolate, a phylogenetic tree was generated by using an alignment of 65 full-length H7 HA sequences obtained from GenBank.

Motivation: Conserved patterns across a multiple sequence alignment can be visualized by generating sequence logos.

We validated the effectiveness of this approach by empirically generating multiple alignments in which motif sites were lost with a frequency determined by our exponential loss function.