In article <170708590S86.SBROWN at GAES.GRIFFIN.PEACHNET.EDU>,
SBROWN at GAES.GRIFFIN.PEACHNET.EDU (Stuart Brown) wrote:
> We have had to deal with the same problem in our core lab. I have found the
> ABI software totally inadequate for sequence assembly and far too time
> consuming for even routine file management of sequences. We have been using
> "Sequencher" from Gene Codes Co. (Ann Arbor, MI) which works fairly well.
> The nicest feature of this program is automatic vector removal. For short
> inserts where you get vector at the 3' end, you can totally ignore the bad
> sequence at the end of the run. For large inserts we usually truncate the
> seq. either automatically at 500 bp, or wherever the "NNN's" start to appear.
> After using the assemble functions and putting together the contigs, we can
> then restore the crummy 3' end sequence to help editing ambiguities. There is
> just no point trying to use bad sequence to assemble contigs.
Take a look at GeneJockeyII. It opens ABI sample files, re-assigns the bases
using the full IUPAC set of degenerate codes, and gives you a graph of the
predicted error rate through your sequence, based on the S/N ratio and
resolution of the sample data. Using this, you can select the 'good bit' of
your sequence, and extract just that into a sequence window for alignment.
It's a general purpose sequence handling program and does lots of other stuff
I declare my interest here since I wrote it.
For a (slightly out of date demo) ftp to s-ind2.dl.ac.uk, or
ftp.embl-heidelberg.de. If you want a more up-to date version call Biosoft
USA : (314) 524 8029
UK : 0223 68622
Phil Taylor | MRC Reproductive Biology Unit
| Centre for Reproductive Biology
| 37 Chalmers Street
mbplt at seqnet.dl.ac.uk | Edinburgh EH3 9EW
ptaylor at hgmp.mrc.ac.uk | Scotland.