Sequence Identification Utilizing Curated Custom Databases

This paper introduces a package, BioDatabase, a web-based application allowing for genetic sequence identification via the creation of custom databases. These custom databases contain a relatively small set of genetic data, specific to a species or a subset for a species. Each custom database sequence contains genetic regions with a highly conserved start and end sequence, along with other specific characteristics defined by an administrator. The package addresses issues regarding GenBank, whose information is valuable, yet difficult to properly utilize due to its size and quality. GenBank’s size also prohibits optimal alignment algorithms from being used when identifying sequences against it. BioDatabase integrates this information, allowing optimal alignment algorithms to be run against local data obtained from GenBank or input manually by a researcher. This maximizes application performance with minimal impact on the speed results are returned to researchers. The BioDatabase package allows researchers to formulate sequence identification concepts and test their ideas against a validated database. Our concluding case study highlights this capability. The case study involves Mycobacterium identification using the 16S and ITS genetic regions. In the case study, researchers were able to correctly identify 72 of 78 Mycobacterium isolates through new sequence identification techniques using the BioDatabase package. These results proved to provide better identification of Mycobacterium in most cases than existing techniques.