Sanger Sequencing Gaps For Genome Closure?

Question

[Neo]

hi all, just wondering if anyone has used sanger sequencing to brige/close the gap between two contigs that have been generated as a result of 454-newbler for prokaryotic genomes?

i.e. when contig reordering programs are used to tile 454 contigs against reference genomes, they tend to push many contigs (genomic regions with repeats, horizontally acquired, unique genes) to the end. to map the location of these contigs to their correct position, has anyone used genomic dna as template and carried out sanger sequencing with primers going outward?

I hope I have not written this question too confusingly. thanks !

Answer 1

[biobot 0.0.77.a.1099]

Yes, this is still common for bridging gaps caused by repeat sequences that are longer than the read length. I was talking to a software developer at the Sanger Institute this week about this; they still use capilliary sequence data in addition to 454 and Illumina.

Answer 2

[2184687-1231-83-]

Is this where the PacBios could be useful? They claim to be able to handle insert sizes of up to 20KB with 1000bp of strobed sequencing that can be distributed at will.