Staden format (again)
Guy Bottu
gbottu at ben.vub.ac.be
Thu Sep 18 09:32:22 UTC 2003
from : BEN
Dear friends,
Excuse me if I am beating a dead horse. I took a look at EMBOSS 2.7.1 and I saw
that Staden and experiment format are still not handled correctly.
Staden format : actually obsolete, the latest version of the Staden package does
not support it anymore. Staden format is a just the sequence in simple text
with, optionally, comments <xxxxx> at any position in the sequence. When
EMBOSS reads in "staden" format, it recognizes only a comment at the top of the
sequence but considers comments inside the sequence as part of the sequence.
Staden experiment format : is used by Staden for assembly. Looks like EMBL
format, but with a lot of extra fields related to the DNA sequencing, and only
one sequence per file is allowed, there can be fields below the "//". EMBOSS
erroneously uses "experiment" as synonym for "staden". You can find more
information about "experiment" format at
http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_18.html
Sincerely,
Guy Bottu
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