help with gap filling - (Feb/28/2011 )

hi,

i am having 454 sequncing data and i have got 6 contigs with that.

also i am having illumina solexa sequences....

Can i use this illumina data for gap filling of the 6 contigs..

i am using geneious software...is there any better plat form for the assembly

(p.S: when i assemble illumina reads,it gives me 361 contigs...)

please help me with this..

dear roshanbernard,

normally gaps in 454 data are caused by repeat regions in the genome (mostly IS elements) that appear more than once in the genome. These sequences are too long that one 454 read can cover them ...this situation can be prevented by using a paired-end library for sequencing. If you want to close the gap you need to do sanger sequencing that will give you reads longer than 1000 bp ...Illumnia reads wont help you much since there appear to be short and do not cover long repeats.

Regards,
p

roshanbernard on Mon Feb 28 08:53:24 2011 said:

Paired end illumina reads with size selected fragments would fill these gaps, likely. Some of the gaps are likely to be from uncertainty in repetitive regions, such as rRNA repeats. Another approach with 6 gaps would be to make outward primers (unique in your contigs) for each fragment, and try the 30 pairs by PCR. You can then sanger sequence the successful pcr reaction products.