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Background In biology, gene identifier conversion is the process of converting gene-related identifiers between different species, strains, or databases. Conversion of identifiers is a critical part of gene identifier mapping. In this paper, we focus on conversion of gene identifiers, e.g., gene names, to other gene identifiers. We propose a method for gene identifier conversion, AbsIDconvert, which consists of two main steps. In the first step, we use the gene identifier mapping relationship to convert the gene identifiers by aligning them to genomic sequences. Then, we convert the gene identifiers to their corresponding identifiers by searching for overlapping intervals. In the second step, we convert gene identifiers to their corresponding identifiers by searching for overlapping intervals. The first step allows us to identify and convert the identifiers by using the genomic interval mapping relationship. In the second step, we convert the gene identifiers by using the genomic interval mapping relationship. AbsIDconvert currently supports ID conversion for 53 species for a given list of input identifiers, genomic sequence, or genome intervals. This tool allows for conversion between identifier domains of interest. The flexibility of AbsIDconvert allows for custom definition of identifier domains contingent upon the availability and determination of a genomic mapping interval. AbsIDconvert is freely available as a web application or downloadable as a virtual machine at: http://bio.kgu.se/absidconvert .

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