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Annotations_List.md

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title Annotations:List
permalink wiki/Annotations%3AList

How do I List the Annotations in a Sequence?

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.

BioJava Annotation objects are a bit like Map objects and they contian key value mappings.

Below is the initial portion of an EMBL file

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).

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.

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();`  
`   }`  
` }`

} ```

Program Output

    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