Absolute ID Conversion Tools

AbIDconvert: Absolute Gene ID Conversion Tools

67 genomes, 66,226,268 gene IDs. All Absolute.

With the availability of gene and protein centric databases (NCBI, Ensembl, UCSC, and others), as well as the wide variety of available platforms for measuring gene expression (Affymetrix, Agilent, custom arrays, and RNA-Seq), biological researchers need reliable methods for converting various identifiers from one type to another. AbsIDConvert is based on the unique idea that genomic identifiers can be converted to genomic intervals, and therefore conversion between identifiers requires simply finding overlapping intervals.

This principle is demonstrated in Figure 1. Here is a region of a genome, with depictions of different genomic entities of varying granularity, including microarray probes, ESTs, transcripts, and loci. By aligning all of these entities to the genome, it becomes simple to convert between them by finding overlapping intervals. In addition, it is also simple to be sure of the correspondence between identifiers.

Figure 1 : ID conversion in AbIDconvert

Finally, storing the data as genomic intervals allows easy updating of the database. More information about the methodology, design, and possible use cases of ABID can be found in the documentation.

ABID allows conversion by identifier, genomic interval, and DNA sequence.

For more information about why ABID improves on other ID conversion tools, please see our paper in BMC Bioinformatics.

Cite: Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC: AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities. BMC Bioinformatics 2012, 13:229. doi:10.1186/1471-2105-13-229.

This work was partially funded by National Institute of Health (NIH) grants P20RR016481, 3P20RR016481-09S1, 8P20GM103436-12 and a Department of Energy (DOE) contract DE-EM0000197. Partial support was also provided by the Paralyzed Veterans of America (fellowship to BJH) and by the Kentucky Spinal Cord and Head Injury Research Trust (JCP). Its contents are solely the responsibility of the authors and do not represent the official views of the funding organizations.