Contigs built with fingerprints, markers, and FPC V4.7

Abstract

Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.

Figure 1

Contig with markers. The markers are ordered by placing each over the deepest stack of positive clones. The markers along the bottom are from the framework map. An * after a clone name indicates a parent clone. The clones highlighted in blue are the tiling path. The clone highlighted in cyan was selected with the mouse, which caused its markers and remarks to be highlighted in green and pink, respectively. The map units are the number of bands.

Figure 2

Consensus band map. In the top row, an = (not shown) or a ˜ indicates a potential exact or approximate buried clone, respectively. Qs indicates a Q (questionable) clone. The next three rows are the clone name. The last row is the number of extra bands that could not be placed. Below these four columns is a set of +, × , and 0. The + signs indicate a band within the tolerance of the consensus band to the right. The × indicate a band within twice the tolerance of the consensus band. The 0 indicate no band within the tolerance.

Figure 3

Gel image and size calculator.

Figure 4

Simulation results with stack of Q clones. A F+ overlap occurs between Zac22_250 and Zac21_61 causing all the sequence 21 clones to end up in a stack, as there is no linear order for both the sequences 22 and 21 clones in the same space. The clones highlighted all have a statistically good overlap with Zac22_250.

Figure 5

Contig from humanmap and sequence. The ZAC clones are highlighted in blue. The two clones highlighted in cyan are the nearest clones from two BAC contigs, as is indicated in the clone text windows, where the oldctg field is the clone's contig previous to the last IBC.