In addition to sequence similarity, the nine sites had a high degree of structure conservation, with similar solvent-accessible surface and secondary structure (Table 3).
In addition to sequence variation, we also observed variation in CRISPR loci in the S. islandicus population that results from spacer loss.
Here, in addition to sequence analysis, we investigated the whole genome composition in H. pylori isolates colonizing the stomachs of infected members of three different families.
This analysis in addition to sequence conservation showed that putative HRE's 1 4 were potential candidates for hypoxia regulatory elements, while HRE-5 lacked sequence conservation and was not further examined by experiments.
Sequence assembly was done with Sequencher (Gene Codes, Ann Arbor, MI, USA) and open reading frames were identified using the ORF finder program at NCBI (http://www.ncbi.nlm.nih.gov/projects/gorf/). Sequence from a portion of a putative 5' LTR was identified in addition to sequence containing regions similar to pol genes from retrotransposons.
Previous work has explored factors in addition to sequence divergence that influence probe hybridization efficiency in different species, such as variation in labeling, overlap of oligonucleotide probes, alternative splicing, sequence homology to non-target transcripts, insertion/deletion differences, and intraspecific polymorphism [33], [34], [39] [43].
Such work emphasized the importance of using richer feature sets (such as secondary structure information in addition to sequence), however, because of the nature of standard single-kernel methods, had to compromise on the type and format of features that could be used.
In addition to sequencing the bedbug's genome, the researchers also looked at gene expression over the bug's life cycle, which spans five instar stages.
One haplotype network was built using chloroplast sequence-based polymorphisms and a second haplotype network was developed using SSR length polymorphisms in addition to sequence-based polymorphisms, where the SSRs were coded as length of PCR amplicon (Doyle et al. [1998]; Hale et al. [2004]).
In addition to sequencing and studying noncoding RNAs, researchers have also been using them as tools to probe gene functions.
In addition to sequencing mtDNA, selected mitochondrial polymorphisms have also been tested for disease association in case-control cohorts [10], [11], [14] [20].
