dbiflat and dbifasta

ableasby at hgmp.mrc.ac.uk ableasby at hgmp.mrc.ac.uk
Wed Aug 9 22:50:06 UTC 2000

In version 1.1.0 (now on the servers) a new database indexing
application has been added (dbifasta). The fasta indexing
has been removed from dbiflat to the new program. The
main reason for this is that there are more fasta formats
than you can shake the proverbial stick at.

Whereas dbiflat used to try and guess the format, dbifasta
requires you to select it. It does allow more formats to be
used though. Specifically:

  >db:ID ACC

Each format can have extra information on the ID line which is
treated as a description. The last listed (ncbi) format assumed
the ID is in the field after the last bar (|). If there is
what looks like a sensible accession number in the preceding
field it will also be indexed otherwise it will be ignored.

Bug fixes in 1.1.0 include dbigcg now accepting SWISS format.
Also, all doc files (so far written) will be installed
correctly (hopefully) and TFM has been modified to look
for them in any specified install directory (or the default
unpack directory).

The ncbi sequence reading has been amended to cope with
variable field numbers.


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