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

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.