Question: Sanger Sequencing Gaps For Genome Closure?
3
gravatar for Neo
8.8 years ago by
Neo200
australia
Neo200 wrote:

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 !

sanger sequencing • 2.2k views
ADD COMMENTlink modified 8.3 years ago by 2184687-1231-83-4.9k • written 8.8 years ago by Neo200
2
gravatar for iw9oel_ad
8.8 years ago by
iw9oel_ad6.0k
iw9oel_ad6.0k wrote:

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.

ADD COMMENTlink written 8.8 years ago by iw9oel_ad6.0k
1
gravatar for 2184687-1231-83-
8.8 years ago by
2184687-1231-83-4.9k wrote:

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.

ADD COMMENTlink written 8.8 years ago by 2184687-1231-83-4.9k
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