Sentence examples for downstream alignment from inspiring English sources
The positional homology alignment facilitates downstream alignment tasks such as phylogenetic inference of nucleotide substitution, phylogenetic inference of gene gain and loss [55], phylogenetic inference of rearrangement [64], and even inference of homologous recombination-induced lateral gene transfer [71].
Each of these reported genomic regions/region pairs are analyzed separately within the downstream alignment pipeline.
Although valuable novel genes are likely to be found there, the incomplete state of assembly in this region makes downstream alignment based analyses problematic.
Inadequate coverage, together with errors occurring in downstream alignment and variant calling, reduces the ability to accurately identify and characterize variants.
Using Geneious, contigs were annotated and sequences in which stop-codons interrupted the open reading frames (potentially representing sequencing artifacts or pseudogenes), or sequence fractions with stop codons located external to the venom domain of interest were removed from downstream alignments.
This was also supported by approximately unbiased topology tests (Shimodaira and Hasegawa 1999), based on the intron or downstream alignments, which rejected the placement of the New World monkeys RLN gene as sister to the RLN1 gene of apes (P < 0.001).
For example, if the annotated interval of genes in the zebra finch genome was expanded by 2,000 bp upstream and downstream then alignments of willow warbler reads overlapped with an additional 1,703 annotated genes.
In the two cases, positioning was stricter downstream (+1 N alignment) than upstream (−1 N alignment) from the NDR, probably due to the variable distance of other upstream NDRs and genes that set the nucleosomal arrays out of phase in the aggregated profiles.
Because adding or deleting 10 bases will shift the homologous sequences by 10, bases will be out of alignment downstream of the shift, making sequencing difficult.
A number of putative TFBS sites, including NF1, AP2, and several SP1 sequences, are in conserved in the alignment downstream of the TSS sites.
For each hit, 600 bp of sequence upstream and downstream of the alignment was used to search for a near-perfect reverse complement (miRNA*) sequence with the miRanda algorithm.
