Advice sought on alternative chemistries

James Bonfield jkb at
Mon Oct 30 06:14:36 EST 1995

There  is   growing  interest    in using     "alternative  sequencing
chemistries"   instead of  sequencing   DNA on both    strands. We are
therefore planning to treat  readings obtained using these alternative
chemistries  in  special ways within  our  assembly  program gap4. For
example, regions covered by such  readings could  be counted as having
data on both strands.

Obviously this will require  a change to  the database (which need not
concern users), but we also need a method of supplying the information
about the  type of sequencing  chemistry used to gap4. One possibility
is to add a new record type to experiment files,  and the simplest and
most general is to assign  a non-zero number  to all readings obtained
using methods that users wish to be considered as  special.  If it was
convenient, this  information could be stored in  the SCF file as well
and be added from there to the corresponding experiment file.

In  the SCF file  we could have a  comment  with code CHEM  and in the
experiment file  a CH  record.  Obviously these  records  will not  be
obligatory and  any reading reaching gap4 without  a CH record will be
treated as standard data.

For example in the SCF file CHEM=1
and in the expt file
CH   1

Please send us any  comments you have about  this, plus the names  and
references   of  sequencing chemistries that  you   would  like to  be
considered as special.

James Bonfield, Kathryn Smith and Rodger Staden

James Bonfield (jkb at   Tel: 01223 402499   Fax: 01223 412282
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.

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