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Automated FingerPrint Background removal: FPB

DOI: 10.1186/1471-2105-10-127

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Abstract:

At the moment, the only tools available for such a task are GenoProfiler and its descendant FPMiner. The large variation in the quality of fingerprints that is usually present in large fingerprinting projects represents a major difficulty in the correct removal of background peaks that has only been partially addressed by the methods so far adopted that all require a long manual optimization of parameters. Thus, we implemented a new data-independent tool, FPB (FingerPrint Background removal), suitable for large scale projects as well as mapping of few clones.FPB is freely available at http://www.appliedgenomics.org/tools.php webcite. FPB was used to remove the background from all fingerprints of three grapevine physical map projects. The first project consists of about 50,000 fingerprints, the second one consists of about 70,000 fingerprints, and the third one consists of about 45,000 fingerprints. In all cases a successful assembly was built.The construction of a whole-genome physical map [1-6] has been an essential component of numerous genome projects initiated since the inception of the Human Genome Project [7]. Its usefulness has been proved for whole-genome shotgun projects as a post-assembly validation and recently it has also been used in the assembly step to constrain on BACs positions [8].High-throughput fingerprinting can produce thousands of BAC clone fingerprints per day. Hence automatic editing of corresponding files can be extremely useful.From now on the description of the process will be based on fingerprints produced on Applied Biosystems Instruments (ABI) automated DNA sequencers, but the method can be applied to any kind of fingerprint as long as similar input is provided. Moreover, the following terms will be used interchangeably since they correspond to the same entity: fragment, band, and peak.Fingerprint data is stored in electrochromatograms, i.e. fsa files, output by GeneMapper, ABI sequencer software. Each peak represents a fragment with a

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