xbap and tiling

Stephen Baird sbaird at mgcheo.med.uottawa.ca
Tue Jan 10 13:02:51 EST 1995

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,

| Stephen Baird                        sbaird at mgcheo.med.uottawa.ca  | 
| Molecular Genetics                       tel: 613-738-3925         |
| Children's Hospital of Eastern Ontario   fax: 613-738-4833         |
| 415 Smyth Rd.                                                      |
| Ottawa, Ontario                                                    |
| Canada                                                             |
| K1H 8M8                                                            |

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