Working with BioJava-live SVN build 4716
Sequence case is not preserved. Line length varies (default is 80 cpl).
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.
Not supported (INSD is).
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
* 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.