[Biojava-dev] Please help with Features and Annotations?

[Michael Griffith]

Mark, 

Thanks for the reply.

Some follow on questions...

If you were to look at the NCBI GenBank record:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=nucleotide&uid=314
18377&dopt=GenBank

Are things like these below considered to be annotations or features?

LOCUS       BC053409                2172 bp    mRNA    linear   ROD
19-NOV-2003
DEFINITION  Mus musculus Unknown (protein for MGC:60843), mRNA (cDNA clone
            MGC:60843 IMAGE:30076516), complete cds.
ACCESSION   BC053409
VERSION     BC053409.1  GI:31418377
KEYWORDS    MGC.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus

Things like:
 gene            1..2172
                     /gene="MGC60843"
                     /db_xref="LocusID:380798"

I would consider features for sure.

If I were to create a Sequence with XXXTools classes, and wrap it in a
ViewSequence, I am not clear on how I might add the DEFINITION or GI, which
appears as a sub-element of VERSION.  Most of the examples deal with how to
manipulate the sequence string itself.

If you (or someone can help me understand this better, I would be willing to
write some demo programs to include, or contribute to the documentation
effort related to this topic.

Again, thanks for your reply.

Cheers!

Michael Griffith


On 9/1/04 8:56 PM, "mark.schreiber at group.novartis.com"
<mark.schreiber at group.novartis.com> wrote:

> Hi Michael -
> 
> The problem with the createDNASequence() method is that is creates a
> Sequence with an Annotation.EMPTY_ANNOTATION place holder for the
> annotation of the Sequence. This Annotation is empty (as the name
> suggests) and cannot be modified so any sequence made this way cannot be
> annotated. 
> One way around this is to create a ViewSequence that wraps the Sequence
> and can have an Annotation added to it. If you read a sequence from a flat
> file (eg fasta) you can add an Annotation to it. Finally if you want to
> add Annotations another approach is to create a SimpleSequence and supply
> it with a SymbolList, Name, URN (can be "" or null) and an Annotation
> (which could be EMPTY_ANNOTATION or SimpleAnnotation or any implementation
> of Annotation). 
> 
> This is a good example of how the static XXXTools methods are convenient
> but don't expose the full flexibility of the biojava API. If you want to
> see how some of that flexibility can be used it can be good to look at the
> code behind the static methods. This reveals how the full API is used and
> shows areas where you can borrow that code and customize it to your needs.
> Eg it would be v simple to write a method for you program that borrows
> code from DNATools.createDNASequence() and takes an Annotation as an
> argument.
> 
> Finally, the Annotation and Feature examples on the BJIA page
> (http://www.biojava.org/docs/bj_in_anger/) may be useful. This link also
> shows how to make a program that views the Annotation and Feature
> structure in a JTree
> (http://www.biojava.org/docs/bj_in_anger/treeView.htm)
> 
> - Mark
> 
> 
> 
> 
> 
> 
> 
> Michael Griffith <mg at base-pair.com>
> Sent by: biojava-dev-bounces at portal.open-bio.org
> 09/02/2004 06:57 AM
> 
> 
>       To:     <biojava-dev at biojava.org>
>       cc: 
>       Subject:        [Biojava-dev] Please help with Features and Annotations?
> 
> 
> Yikes! Is there a good explanation somewhere on Features and annotations?
> I
> am creating a new Sequence using the DNATools.createDNASequence() method,
> but I want to set some features on it like the GI # and the DEFINITION.  I
> can't seem to figure out how this works.
> 
> Any help would be greatly appreciated!
> 
> MG
> 
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> 
>