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The construction of a whole-genome physical map has been an essential component of numerous genome projects initiated since the inception of the Human Genome Project. 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.
Fingerprinting is usually the method of choice for construction of physical maps. A clone fingerprint is composed of true peaks representing real fragments and background peaks, mainly composed of E. coli genomic DNA, partial digestions, and machine background. High-throughput fingerprinting leads to the production of thousands of BAC clone fingerprints per day. That is why background peaks removal has become an important issue and needs to be automatized, especially in polyacrylamide-gel based fingerprints.
At the moment, the only tools available for such a task are GenoProfiler and its descendant FPMiner, that we believe highly data dependent programs and therefore lack of accuracy on large projects.
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 www.appliedgenomics.org/tools.php.