EMBOSS 1.9.0

ableasby at hgmp.mrc.ac.uk ableasby at hgmp.mrc.ac.uk
Mon Jan 22 17:25:21 UTC 2001

EMBOSS 1.9.0 is now available. New applications appear
below (I may have missed some out but my colleagues will
no doubt post if I have).

Installation amendment: some sites were experiencing difficulties
  with autoconf. This was usually manifested by problems installing
  the ACD files. The installation files have been adjusted to
  solve this.

List file reading: programs will now just give a warning for
  bad '@'file entries and carry on reading the list. This
  previously caused program termination

Programming libraries: linked lists are now doubly linked. List
  iteration and string iteration functions have been rewritten.

This application scans a given nucleotide sequence for restriction
sites. It reports single base positions in the restriction pattern which

when mutated remove the restriction site whilst maintaining the same
translation. Several restriction enzymes can be specified or
alternatively all the enzymes in the REBASE database can be
investigated. To find out whether the single point mutations found by
'recode', introduce new restriction sites, 'silent' should be run on the

original sequence. ('Silent' searches for silent point mutation sites
which maintain the same translation, see 'silent' documentation). The
output for 'recode' is similar to the format used by 'silent'.

This program graphically displays the results in an ABI file. The data
for each nucleotide is plotted and the assigned nucleotide (G, A, T, C
or N) in the ABI file is overlayed on the graphs.


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