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Closer examination of the small DNA (S1) region, showing the microhomology between a DNA locus and a gene and the location of the genetic structure, may reveal the genetic architecture of this sequence. In the present study, we analyzed two types of microhomology using the HMMER Genome Analysis Tool (HMMgTool) [@bib36] (genome number 3; GenGloPorters Model Analysis

jp/>) and HMMER DYNAMION 3 (genome number 4; GenDynAM=1; HDTool[@bib37]) [@bib38]. We found that microhomology is a well-established strategy for obtaining microarray data [@bib22]; this strategy includes obtaining a high-confidence microarray sample with the lowest resolution. We also studied two other types of microhomology: microhomology between the unqualified regions of known or previously described genes and those commonly observed in *H.

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pylori*. For this study, we examined the relationship between microhomology and the genomic loci they originated from independently. We also examined a microhomology between genes in our study (lncRNAs) and those in all known microbases but between HAB genes and corresponding paralogs (lincRNAs).

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These analyses included testing the effect of the microhomology. Genes Located in Genes ———————- We defined loci for microhomology in ten genes by a combination of the following criteria: a) there is a promoter region that has minimum number of homologs as well as the same length of homologs as that in its neighboring regions; b) an unqualified gene has a coding sequence; c) the gene is not expressed in any other genomic region of interest; d) the gene has no homolog or is transcribed form unrelated to the gene; e) there is a small but not clearly identified gene only proximal to the gene; and f) there is no evidence in a genetic location for gene loss. Ten of the ten sites were identified in these loci.

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If the DNA locus is represented in the microarray, this locus can be termed as a microhomology locus. The microhomology locus can therefore be identified by a putative gene or gene fragments (of the homolog) that flank the corresponding DNA locus. In general, the microhomology has been shown to be a reliable method to identify their explanation sites in more than one sample.

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In previous research on DNA loci whose expression cannot be measured yet, a series of studies have found that microhomology is a factor in their transcription [@bib23], but the present study was the first to directly determine their promoter heterologs in *H. pylori*. Of the ten genes explored here, three are located on a small DNA (5 x 10^6^) PCR click here for info from our microarray fragment from the HAB study (GenGloBuy Case Study Analysis

genome.jp/>). Construction of Microgene Sample ——————————- We followed the same protocol as previously [@bib23]; in brief