Scaffolds

[nitinkumar]

I want to compare the scaffolds with the reference sequence and analyze the order and orientation. Can any body help me in this? also can we close gaps in the scaffolds using bioinformatics approach

[Raj]

Hi,
This maybe a bit late, I was just browsing the 454 forum for something else...anyways, if its still of use:
For comparing scaffolds with a reference genome you can:
Use roche reference mapper (part of newbler), MAUVE, Artemis comparison tool and contig aligner an online program http://nbc11.biologie.uni-kl.de/fram...ontig_aligner/.

They involve you uploading/submitting your reference genome as fasta file and your concatentated scaffolds (merge all your scaffolds into a single fasta file) or individually uploading/submitting them as a seperate 'genome/s'. Note the positions so you can work out the order.

For gap closing informatically i don't know of any sure way of doing it, i've tried by blast searching and using contig aligner to compare the unmapped contigs to the reference genome to see where they match, for us the ones that were confidently mapped were experimentally confirmed. This in some instances closed gaps but in the majority reduced the gap size for experimental closure, primer walking etc... But again i'm not sure of a fool-proof method to do it bioinformatically...