<h2 id="how-do-i-list-the-annotations-in-a-sequence">How do I List the Annotations in a Sequence?</h2>

<p>When you read in a annotates sequence file such as GenBank or EMBL there

is a lot more detailed information in there than just the raw sequence.

If the information has a sensible location then it ends up as a Feature.

If it is more generic such as the species name then the information ends

up as Annotations.</p>

<p>BioJava Annotation objects are a bit like Map objects and they contian

key value mappings.</p>

<p>Below is the initial portion of an EMBL file</p>

<div class="highlighter-rouge"><pre class="highlight"><code>ID AY130859 standard; DNA; HUM; 44226 BP.

XX

AC AY130859;

XX

SV AY130859.1

XX

DT 25-JUL-2002 (Rel. 72, Created)

DT 25-JUL-2002 (Rel. 72, Last updated, Version 1)

XX

DE Homo sapiens cyclin-dependent kinase 7 (CDK7) gene, complete cds.

XX

KW .

XX

OS Homo sapiens (human)

OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;

OC Eutheria; Primates; Catarrhini; Hominidae; Homo.

XX

RN [1]

RP 1-44226

RA Rieder M.J., Livingston R.J., Braun A.C., Montoya M.A., Chung M.-W.,

RA Miyamoto K.E., Nguyen C.P., Nguyen D.A., Poel C.L., Robertson P.D.,

RA Schackwitz W.S., Sherwood J.K., Witrak L.A., Nickerson D.A.;

RT ;

RL Submitted (11-JUL-2002) to the EMBL/GenBank/DDBJ databases.

RL Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA

RL 98195, USA

XX

CC To cite this work please use: NIEHS-SNPs, Environmental Genome

CC Project, NIEHS ES15478, Department of Genome Sciences, Seattle, WA

CC (URL: http://egp.gs.washington.edu).

<p>The following program reads an EMBL file and lists its Annotation

properties. The output of this program on the above file is listed below

the program.</p>

<java> import java.io.\*; import java.util.\*;

import org.biojava.bio.\*; import org.biojava.bio.seq.\*; import

org.biojava.bio.seq.io.\*;

public class ListAnnotations {

` public static void main(String[] args) {`

`   try {`

`     //read in an EMBL Record`

`     BufferedReader br = new  BufferedReader(new FileReader(args[0]));`

`     `

`     //for each sequence list the annotations`

`     for(SequenceIterator seqs = SeqIOTools.readEmbl(br); seqs.hasNext(); ){`

`       Annotation anno = seqs.nextSequence().getAnnotation();`

`       //print each key value pair`

`       for (Iterator i = anno.keys().iterator(); i.hasNext(); ) {`

`         Object key = i.next();`

`         System.out.println(key +" : "+ anno.getProperty(key));`

`       }`

`     }`

`   }`

`   catch (Exception ex) {`

`     ex.printStackTrace();`

`   }`

` }`

} </java>

<p>Program Output</p>

<div class="highlighter-rouge"><pre class="highlight"><code>RN : [1]

KW : .

RL : [Submitted (11-JUL-2002) to the EMBL/GenBank/DDBJ databases., Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA, 98195, USA]

embl_accessions : [AY130859]

DE : Homo sapiens cyclin-dependent kinase 7 (CDK7) gene, complete cds.

SV : AY130859.1

AC : AY130859;

FH : Key Location/Qualifiers

XX :

OC : [Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;, Eutheria; Primates; Catarrhini; Hominidae; Homo.]

RA : [Rieder M.J., Livingston R.J., Braun A.C., Montoya M.A., Chung M.-W.,, Miyamoto K.E., Nguyen C.P., Nguyen D.A., Poel C.L., Robertson P.D.,, Schackwitz W.S., Sherwood J.K., Witrak L.A., Nickerson D.A.;]

ID : AY130859 standard; DNA; HUM; 44226 BP.

DT : [25-JUL-2002 (Rel. 72, Created), 25-JUL-2002 (Rel. 72, Last updated, Version 1)]

CC : [To cite this work please use: NIEHS-SNPs, Environmental Genome, Project, NIEHS ES15478, Department of Genome Sciences, Seattle, WA, (URL: http://egp.gs.washington.edu).]

RT : ;

OS : Homo sapiens (human)

RP : 1-44226