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MCL, FMY, and NH analyzed fingerprints, assembled the physical map, and verified assembly.
Specifically, we asked whether the alignments of verified assembly products overlapped with any other verified assembly product that had been assigned the same orthology.
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J HM analyzed fingerprints, assembled the physical map, verified contig assembly and wrote the manuscript.
SQ conceived the project, developed the protocols for DNA extraction and fingerprinting on the 3730 xl Analyzer, obtained the fingerprints, assembled the physical map, verified contig assembly and wrote the manuscript draft.
SMY: verified SOAPdenovo assembly results by Trinity and revised the manuscript.
> -wrap-foot> Finally, we verified that assembly errors in the form of contigs consisting of incorrectly ordered genes do not exist in any of our mt genome assemblies.
We verified unigene assembly by mapping all reads to the genome with BLAT and testing whether the unassembled reads of a contig mapped to the same genome location as the contig.
Genome assemblies rely on the existence of transcript sequence to stitch together contigs, verify assembly of whole genome shotgun reads, and annotate genes.
In several instances, our experimentally verified transcript assemblies overlapped multiple Twinscan or EuGene predictions, such as neighboring genes At.chr4.2.13 and At.chr4.2.14.
To verify our assembly further, we performed a second pass assembly using Minimus [ 22], which gave an assembly with an N50 value of 1678 bp.
The accuracy of the CLC assembly was further verified using another assembly tool, Velvet [ 28], and by mapping the reads back to the contigs.
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