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. 2005 Jul 1;33(Web Server issue):W560-6.
doi: 10.1093/nar/gki356.

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies

Sacha A F T van Hijum  1 , Aldert L Zomer, Oscar P Kuipers, Jan Kok
Affiliations

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies

Sacha A F T van Hijum et al. Nucleic Acids Res. .

Abstract

With genome sequencing efforts increasing exponentially, valuable information accumulates on genomic content of the various organisms sequenced. Projector 2 uses (un)finished genomic sequences of an organism as a template to infer linkage information for a genome sequence assembly of a related organism being sequenced. The remaining gaps between contigs for which no linkage information is present can subsequently be closed with direct PCR strategies. Compared with other implementations, Projector 2 has several distinctive features: a user-friendly web interface, automatic removal of repetitive elements (repeat-masking) and automated primer design for gap-closure purposes. Moreover, when using multiple fragments of a template genome, primers for multiplex PCR strategies can also be designed. Primer design takes into account that, in many cases, contig ends contain unreliable DNA sequences and repetitive sequences. Closing the remaining gaps in prokaryotic genome sequence assemblies is thereby made very efficient and virtually effortless. We demonstrate that the use of single or multiple fragments of a template genome (i.e. unfinished genome sequences) in combination with repeat-masking results in mapping success rates close to 100%. The web interface is freely accessible at http://molgen.biol.rug.nl/websoftware/projector2.

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Figures

Figure 1
Figure 1
The Projector 2 procedure. From top to bottom: I, single (left) or fragmented n-multiple templates (right) are optionally repeat masked; II, contigs (middle) are fragmented and also optionally repeat masked; III, the (unique) contig fragments are compared against the (unique) template fragments using BLAST; yielding IV, mapped contigs. Arrows with a plus sign (+) signify contigs that were successfully mapped; and those with a minus (−) sign could not be mapped. V, For the mapped contigs, gap-closing sequences and PCR primers are designed and a visual SVG output is generated.
Figure 2
Figure 2
SVG output of Projector 2 runs performed with and without repeat-masking. (A–D) Details of the results for mapping of: (A) R.typhi contigs on its isogenic template; (B) N.europaea contigs on its isogenic template; (C) L.lactis MG1363 contigs on L.lactis IL1403; and (D) M.tuberculosis contigs on M.tuberculosis. For each inset, the mapping results with (lower panel) and without (upper panel) repeat-masking of the target and template sequences are shown. A ruler in base pairs (kb or Mb) is shown above each mapping. The template fragments are indicated in dark green triangles below this scale. The mapped contigs, one or at most two on each line, are shown below the template fragments. Within each mapped contig, the L and R fragments used to map the contig are indicated with green boxes. Contig numbers are shown for mapping in (D). A dot (•) indicates an incorrectly mapped contig on that line.
Figure 3
Figure 3
Results of the mapping procedures described in Table 2. The percentage of mapped contigs is plotted for four bacterial genome assemblies mapped onto (non-) isogenic templates (for details see Table 2).
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