BioJava

• Working with BioJava?-live SVN version 4723.

Fasta Format

Major Issues

• None

Minor Issues

• Sequence case is not preserved. --not really a bug. It is preserved if you pass in a masked alphabet instead of the default DNA alphabet.
• Line length varies (default is 80 cpl).

===Read-Write-Read===

• Succeeds!

Genbank format

Major Issues

• None.

Minor Issues

• Feature qualifier order is not preserved. --it is, but xrefs and organism are moved to end of list as they are not stored internally as qualifiers.
• 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. ===Read-Write-Read===

• Success!

GenbankXML format

Major Issues

• Not supported (INSD is).

INSD Format

Major Issues

• None.

Minor Issues

• 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. --see Genbank

===Read-Write-Read===

• Success!

EMBL Format

Major Issues

• No major issues

Minor Issues

• Version in date is not correct on output. --fixed
• Two XX lines after references. -- fixed
• Feature qualifiers out of order. --see Genbank

===Read-Write-Read===

• Succeeds!

SwissProt/ Uniprot

Major Issues

Minor Issues

• BioSQL cannot store more than one database reference for a single publication,

eg Pubmed and medline Id and DOI.

• We are putting 'and' before the last author. --fixed
• We loose the copyright statement. -- fixed

===Read-Write-Read===

• Cannot read back in: -- fixed

<code> Format_object=org.biojavax.bio.seq.io.UniProtFormat? Accession=Q43385 Id= Comments= Parse_block=OS Arabidopsis thaliana (Mouse-ear cress) (Arabidopsis thaliana (L.) Heynh.).OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;OS Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.OX NCBI_TaxID=3702; Stack trace follows ....

at org.biojavax.bio.seq.io.UniProtFormat?.readRichSequence(UniProtFormat?.java:615) at org.biojavax.bio.seq.io.RichStreamReader?.nextRichSequence(RichStreamReader?.java:110) ... 3 more

Caused by: java.lang.IllegalArgumentException?: NCBI taxonomy names cannot embed new lines - at:74, in name: <Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis>

at org.biojavax.bio.taxa.SimpleNCBITaxonName.<init>(SimpleNCBITaxonName.java:47) at org.biojavax.bio.taxa.SimpleNCBITaxon.addName(SimpleNCBITaxon.java:148) at org.biojavax.bio.seq.io.UniProtFormat?.readRichSequence(UniProtFormat?.java:339) ... 4 more

</code>

UniprotXML

Major Issues

• Missing the namespace and the version from entry tag -- fixed
• Don't write editor list if there are no editors -- fixed
• Reference tag not correctly constructed. -- fixed
• When writing Uniprot XML it would be illegal to use anything other than

Swiss-Prot or TrEMBL as the Namespace -- fixed but only if record originally had correct NS

** NEW ISSUES

• Missing 'proteinExistence' tag before first keyword.
• Missing 'version' attribute on sequence tag. This is distinct from entry version - entry version needs to be moved to an annotation.

Minor Issues

===Read-Write-Read===

EMBLxml

Major Issues

• none

Minor Issues

===Read-Write-Read===

• Success!