= !BioJava =
Working with !BioJava-live SVN build 4716

== Fasta Format ==
=== Major Issues ===
None
=== Minor Issues ===
Sequence case is not preserved. Line length varies (default is 80 cpl).


== Genbank format ==
=== Major Issues ===
None.
=== Minor Issues ===
Feature qualifier order is not preserved.
Because NCBI Taxonomy is referenced from memory or database if the version used
doesn't match the version that was used to construct the record then minor 
differences appear. For example the common name of Arabidopsis changed from thale cress
to mouse ear cress.

== GenbankXML format ==
== Major Issues ==
Not supported (INSD is).

== INSD Format ==
== Major Issues ==
None.
== Minor Issues ==
Biojava doesn't add the XML header and INSDSet tags, starts with INSDSeq.
{{{
<?xml version="1.0"?>
<!DOCTYPE INSDSet PUBLIC "-//NCBI//INSD INSDSeq/EN" "http://www.ncbi.nlm.nih.gov/dtd/INSD_INSDSeq.dtd">
<INSDSet>
<INSDSeq>
...
}}}

* !BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..1
{{{
<INSDReference_position>1..1</INSDReference_position>
}}}

* There are other examples of this redundancy. I think if this doesn't break the
dtd then it doesn't matter.

* Qualifiers order is not preserved. I don't think this matters.