Subject: xbap and tiling
Newsgroups: bionet.software.staden
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Rodger Staden, James Bonfield and Staden users,
I having been using Xbap quite a bit and unfortunately it has one
shortcoming which I would like to see changed. I've gotten use to any
other problems. I started using a sequencing strategy published by Chen,
E.Y. et al. which cuts up large fragments of DNA (40kb and up) into
random 5kb plasmids. You sequence the ends of a certain number of these (
statistically determined)plasmids and you can get a tiling pattern of the
minimum number of plasmids needed to sequence the complete fragment.The
sequencing of each plasmid can be done with some sort of ordered deletion
method. Unfortunately creating the tiling pattern takes a bit of manual
labour since XBAP will only create contigs with the ends treated as
separate reads not as being connected. I'd like to see sample1.T3 and
sample1.T7 being treated as a connected sequence with a gap in it. This
shotgun/ordered approach seems to me to be the best sequencing strategy
at the time for sequencing Yacs and Pacs so would it not be useful to
add the tiling feature in the contig building?
I have not tried XGAP so I do not know if there is a way to do
this using it. If there is a way to do this contig building to create a
tiling pattern with the existing software I would love to know?
eagerly awaiting all replies,
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| Stephen Baird sbaird at mgcheo.med.uottawa.ca |
| Molecular Genetics tel: 613-738-3925 |
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