<h2 id="biojava-30-release">BioJava 3.0 release</h2>

<p>Many things changed in the BioJava 3.0 release. The cookbook for the new

API is available from here: <biojava:cookbook3.0> The content on this

page is still available to support the legacy code base, which is now

available through the biojava-legacy project in the BioJava SVN.</biojava:cookbook3.0></p>

<h2 id="biojava-in-anger---a-tutorial-and-recipe-book-for-those-in-a-hurry">BioJava In Anger - A Tutorial and Recipe Book for Those in a Hurry</h2>

<p>BioJava can be both big and intimidating. For those of us who are in a

hurry there really is a whole lot there to get your head around. This

document is designed to help you develop BioJava programs that do 99% of

common tasks without needing to read and understand 99% of the BioJava

API.</p>

<p>The page was inspired by various programming cookbooks and follows a

“How do I…?” type approach. Each “How do I?” is linked to some example

code that does what you want and sometimes more. Basically if you find

the code you want and copy and paste it into your program you should be

up and running quickly. I have endeavoured to over document the code to

make it more obvious what I am doing so some of the code might look a

bit bloated.</p>

<p>If you have any suggestions, questions or comments contact the <a href="&#109;&#097;&#105;&#108;&#116;&#111;:&#098;&#105;&#111;&#106;&#097;&#118;&#097;&#045;&#108;&#064;&#098;&#105;&#111;&#106;&#097;&#118;&#097;&#046;&#111;&#114;&#103;">biojava

mailing list</a>. To subscribe to this list

go <a href="http://biojava.org/mailman/listinfo/biojava-l">here</a></p>

<p>If you re-use code from the cookbook please cite:</p>

<h2 id="announcing">Announcing</h2>

<p>You can now read BioJava in Anger in

<a href="Biojava:CookbookFrench" title="wikilink">French</a> (Translated by Sylvain

Foisy; mise à jour / updated : 28 décembre 2009).</p>

<p>You can also read Biojava in Anger in

<a href="Biojava:CookbookPortuguese" title="wikilink">Portuguese</a> (Translated by

Dickson Guedes)</p>

<p>You can also read BioJava in Anger in

<a href="http://www.geocities.jp/bio_portal/bj_in_anger_ja/">Japanese</a>

(Translated by Takeshi Sasayama and Kentaro Sugino, updated 14 Aug

2004).</p>

<p>How about simplified

<a href="http://www.cbi.pku.edu.cn/chinese/documents/PUMA/biojava/index-cn.html">Chinese</a>?

(Translated by Wu Xin).</p>

<p>And lets not forget this new

<a href="BioJava:CookBookItaliano" title="wikilink">Italian</a> translation (translated

by Alessandro Cipriani; last update: 9 Sep 2010).</p>

<h2 id="how-do-i">How Do I….?</h2>

<h3 id="setup">Setup</h3>

<li><a href="http://java.sun.com/javase/downloads/index.jsp">Where do I get a Java

installation</a>?</li>

<li><a href="BioJava:GetStarted" title="wikilink">How do I get and install BioJava</a>?</li>

<h3 id="alphabets-and-symbols">Alphabets and Symbols</h3>

<li><a href="Biojava:Cookbook:Alphabets" title="wikilink">How do I get a DNA, RNA or Protein

Alphabet</a>?</li>

<li><a href="Biojava:Cookbook:Alphabets:Custom" title="wikilink">How do I make a custom Alphabet from custom

Symbols</a>?</li>

<li><a href="Biojava:Cookbook:Alphabets:CrossProduct" title="wikilink">How do I make a CrossProductAlphabet such as a codon

Alphabet</a>?</li>

<li><a href="Biojava:Cookbook:Alphabets:Component" title="wikilink">How do I break Symbols from CrossProduct Alphabets into their

component Symbols</a>?</li>

<li><a href="Biojava:Cookbook:Alphabets:Cononical" title="wikilink">How can I tell if two Alphabets or Symbols are

equal</a>?</li>

<li><a href="Biojava:Cookbook:Alphabets:Ambiguous" title="wikilink">How can I make an ambiguous Symbol like Y or

R</a>?</li>

<h3 id="basic-sequence-manipulation">Basic Sequence Manipulation</h3>

<li><a href="Biojava:Cookbook:Sequence" title="wikilink">How do I make a Sequence from a String or make a Sequence Object

back into a String</a>?</li>

<li><a href="Biojava:Cookbook:Sequence:SubSequence" title="wikilink">How do I get a subsection of a

Sequence</a>?</li>

<li><a href="Biojava:Cookbook:Sequence:Transcribe" title="wikilink">How do I transcribe a DNA Sequence to a RNA

Sequence</a>?</li>

<li><a href="Biojava:Cookbook:Sequence:Reverse" title="wikilink">How do I reverse complement a DNA or RNA

Sequence</a>?</li>

<li><a href="Biojava:Cookbook:Sequence:ChangeName" title="wikilink">Sequences are immutable so how can I change it’s

name</a>?</li>

<li><a href="Biojava:Cookbook:Sequence:Edit" title="wikilink">How can I edit a Sequence or

SymbolList</a>?</li>

<li><a href="Biojava:Cookbook:Sequence:Regex" title="wikilink">How can I make a sequence motif into a regular

expression</a>?</li>

<li><a href="Biojava:Cookbook:Sequence:ExtractGeneRegions" title="wikilink">How can I extract all regions beeing marked (or not) with a special

feature (e.g. ‘gene’ or

‘CDS’)</a>?</li>

<h3 id="translation">Translation</h3>

<li><a href="Biojava:Cookbook:Translation" title="wikilink">How do I translate a DNA or RNA Sequence or SymbolList to

Protein</a>?</li>

<li><a href="Biojava:Cookbook:Translation:Single" title="wikilink">How do I translate a single codon to a single amino

acid</a>?</li>

<li><a href="Biojava:Cookbook:Translation:NonStandart" title="wikilink">How do I use a non standard translation

table</a>?</li>

<li><a href="Biojava:Cookbook:Translation:SixFrames" title="wikilink">How do I translate a nucleotide sequence in all six

frames</a>?</li>

<li><a href="Biojava:Cookbook:Translation:OneLetterAmbi" title="wikilink">How do I retrieve the 1-Letter code of a translated sequence

containing

ambiguities</a>?</li>

<h3 id="proteomics">Proteomics</h3>

<li><a href="Biojava:Cookbook:Proteomics" title="wikilink">How do I calculate the mass and pI of a

peptide</a>?</li>

<li><a href="Biojava:Cookbook:Proteomics:AAindex" title="wikilink">How do I analyze the symbol properties of an amino acid sequence

using the Amino Acid Index

database</a>?</li>

<h3 id="sequence-io">Sequence I/O</h3>

<li><a href="Biojava:Cookbook:SeqIO:WriteInFasta" title="wikilink">How do I write Sequences in Fasta

format</a>?</li>

<li><a href="Biojava:Cookbook:SeqIO:ReadFasta" title="wikilink">How do I read in a Fasta

file</a>?</li>

<li><a href="Biojava:Cookbook:SeqIO:ReadGES" title="wikilink">How do I read a GenBank/EMBL/SwissProt

file</a>?(deprecated)</li>

<li><a href="Biojava:Cookbook:SeqIO:ReadGESBiojavax" title="wikilink">How do I read a GenBank/EMBL/UniProt/FASTA/INSDseq

file</a>?</li>

<li><a href="Biojava:Cookbook:SeqIO:GBtoFasta" title="wikilink">How do I extract GenBank/EMBL/UniProt/FASTA/INSDseq sequences and

write them as Fasta</a>?</li>

<li><a href="Biojava:Cookbook:SeqIO:ABItoSequence" title="wikilink">How do I turn an ABI sequence trace into a BioJava

Sequence</a>?</li>

<li><a href="Biojava:Cookbook:SeqIO:Echo" title="wikilink">How does sequence I/O work in

BioJava</a>?</li>

<h3 id="annotations">Annotations</h3>

<li><a href="BioJava:Cookbook:Annotations:List" title="wikilink">How do I list the Annotations in a

Sequence</a>?</li>

<li><a href="BioJava:Cookbook:Annotations:List2" title="wikilink">How do I extract Annotations for a set of

Features</a>?</li>

<li><a href="BioJava:Cookbook:Annotations:Filter" title="wikilink">How do I filter a Sequences based on their species (or another

Annotation

property)</a>?</li>

<h3 id="locations-and-features">Locations and Features</h3>

<li><a href="BioJava:Cookbook:Locations:Point" title="wikilink">How do I specify a

PointLocation</a>?</li>

<li><a href="BioJava:Cookbook:Locations:Range" title="wikilink">How do I specify a

RangeLocation</a>?</li>

<li><a href="BioJava:Cookbook:Locations:Circular" title="wikilink">How do CircularLocations

work</a>?</li>

<li><a href="BioJava:Cookbook:Locations:Feature" title="wikilink">How can I make a

Feature</a>?</li>

<li><a href="BioJava:Cookbook:Locations:Filter" title="wikilink">How can I filter Features by

type</a>?</li>

<li><a href="BioJava:Cookbook:Locations:Remove" title="wikilink">How can I remove

features</a>?</li>

<h3 id="blast-and-fasta">BLAST and FASTA</h3>

<li><a href="BioJava:CookBook:Blast:Parser" title="wikilink">How do I set up a BLAST

parser</a>?</li>

<li><a href="BioJava:CookBook:Fasta:Parser" title="wikilink">How do I set up a FASTA

parser</a>?</li>

<li><a href="BioJava:CookBook:Blast:Extract" title="wikilink">How do I extract information from parsed

results</a>?</li>

<li><a href="BioJava:CookBook:Blast:Echo" title="wikilink">How do I parse a large file; Or, How do I make a custom

SearchContentHandler</a>?</li>

<li><a href="BioJava:CookBook:Blast:XML" title="wikilink">How do I convert an XML BLAST result into HTML

page</a>?</li>

<h3 id="counts-and-distributions">Counts and Distributions</h3>

<li><a href="BioJava:CookBook:Count:Residues" title="wikilink">How do I count the residues in a

Sequence</a>?</li>

<li><a href="BioJava:CookBook:Count:Frequency" title="wikilink">How do I calculate the frequency of a Symbol in a

Sequence</a>?</li>

<li><a href="BioJava:CookBook:Count:ToDistrib" title="wikilink">How can I turn a Count into a

Distribution</a>?</li>

<li><a href="BioJava:CookBook:Distribution:RandomSeqs" title="wikilink">How can I generate a random sequence from a

Distribution</a>?</li>

<li><a href="BioJava:CookBook:Distribution:Entropy" title="wikilink">How can I find the amount of information or entropy in a

Distribution</a>?</li>

<li><a href="BioJava:CookBook:Distribution:Emission" title="wikilink">What is an easy way to tell if two Distributions have equal

weights</a>?</li>

<li><a href="BioJava:CookBook:Distribution:Custom" title="wikilink">How can I make an OrderNDistribution over a custom

Alphabet</a>?</li>

<li><a href="BioJava:CookBook:Distribution:XML" title="wikilink">How can I write a Distribution as

XML</a>?</li>

<li><a href="BioJava:CookBook:Distribution:Gibbs" title="wikilink">Using Distributions to make a Gibbs

sampler</a></li>

<li><a href="BioJava:CookBook:Distribution:Bayes" title="wikilink">Using Distributions to make a naive Bayes

classifier</a></li>

<li><a href="Biojava:CookBook:Distribution:Composition" title="wikilink">How do I calculate the composition of a Sequence or collection of

Sequences?</a>

This example uses JDK 1.5 and BioJavaX</li>

<h3 id="weight-matrices-and-dynamic-programming">Weight Matrices and Dynamic Programming</h3>

<li><a href="BioJava:CookBook:DP:WeightMatrix" title="wikilink">How do I use a WeightMatrix to find a

motif</a>?</li>

<li><a href="BioJava:CookBook:DP:HMM" title="wikilink">How do I make a HMMER like profile

HMM</a>?</li>

<li>|How do I set up a custom HMM? (Link to

Tutorial?? –<a href="User:Guedes" title="wikilink">Guedes</a> 11:43, 8 February 2006

(EST) )</li>

<li><a href="BioJava:CookBook:DP:PairWise" title="wikilink">How do I generate a pair-wise alignment with a Hidden Markov

Model</a>?</li>

<li><a href="BioJava:CookBook:DP:PairWise2" title="wikilink">How do I generate a global or local alignment with the

Needleman-Wunsch- or the

Smith-Waterman-algorithm</a>?</li>

<h3 id="user-interfaces">User Interfaces</h3>

<li><a href="BioJava:CookBook:Interfaces:ViewAsTree" title="wikilink">How can I visualize Annotations and Features as a

tree</a>?</li>

<li><a href="BioJava:CookBook:Interfaces:ViewInGUI" title="wikilink">How can I display a Sequence in a

GUI</a>?</li>

<li><a href="BioJava:CookBook:Interfaces:ViewInGUI2" title="wikilink">How can I create a RichSequence

viewer</a>?</li>

<li><a href="BioJava:CookBook:Interfaces:Coordinates" title="wikilink">How do I display Sequence

coordinates</a>?</li>

<li><a href="BioJava:CookBook:Interfaces:Features" title="wikilink">How can I display

features</a>?</li>

<li><a href="BioJava:CookBook:Interfaces:Alignments" title="wikilink">How can I view an

Alignment</a>?</li>

<li><a href="BioJava:CookBook:Interfaces:Alignments II" title="wikilink">How can I view an Alignment

II</a>?</li>

<li><a href="BioJava:CookBook:Interfaces:ProteinPeptideFeatures" title="wikilink">How can I display Protein Features / a Peptide

Digest</a>?</li>

<h3 id="biosql-and-sequence-databases">BioSQL and Sequence Databases</h3>

<li><a href="BioJava:CookBook:BioSQL:SetupPostGre" title="wikilink">How do I set up BioSQL with

PostgreSQL?</a> (by

<a href="User:David" title="wikilink">David Huen</a>)</li>

<li><a href="BioJava:CookBook:BioSQL:SetupOracle" title="wikilink">How do I set up BioSQL with

Oracle?</a> (by

<a href="User:Richard" title="wikilink">Richard Holland</a>)</li>

<li><a href="BioJava:CookBook:BioSQL:Manage" title="wikilink">How do I add, view and remove Sequence Objects from a BioSQL

DB?</a></li>

<li><a href="BioJava:CookBook:ExternalSources:NCBIFetch" title="wikilink">How can I get a sequence straight from

NCBI?</a></li>

<h3 id="external-applications-and-services">External Applications and Services</h3>

<li><a href="BioJava:CookBook:Services:Qblast" title="wikilink">How can I use QBlast to do my alignments

remotely</a>?</li>

<h3 id="genetic-algorithms">Genetic Algorithms</h3>

<li><a href="BioJava:CookBook:GA" title="wikilink">How can I make a Genetic Algorithm with

BioJava</a>?</li>

<h3 id="protein-structure">Protein Structure</h3>

<li><a href="BioJava:CookBook:PDB:read" title="wikilink">How can I parse a PDB file?</a></li>

<li><a href="BioJava:CookBook:PDB:mmcif" title="wikilink">How can I parse a .mmcif

file?</a></li>

<li><a href="BioJava:CookBook:PDB:atoms" title="wikilink">How can I access the atoms in a

structure?</a></li>

<li><a href="BioJava:CookBook:PDB:atomsCalc" title="wikilink">How can I do calculations on

atoms?</a></li>

<li><a href="BioJava:CookBook:PDB:groups" title="wikilink">How to work with Groups (AminoAcid, Nucleotide,

Hetatom)?</a></li>

<li><a href="BioJava:CookBook:PDB:header" title="wikilink">How can I access the header information of a PDB

file?</a></li>

<li><a href="BioJava:CookBook:PDB:seqres" title="wikilink">How does BioJava deal with SEQRES and ATOM

groups?</a></li>

<li><a href="BioJava:CookBook:PDB:mutate" title="wikilink">How can I mutate a

residue?</a></li>

<li><a href="BioJava:CookBook:PDB:align" title="wikilink">How can I calculate a structure

alignment?</a></li>

<li><a href="BioJava:CookBook:PDB:alignGUI" title="wikilink">How can I use a simple GUI to calculate an

alignment?</a></li>

<li><a href="BioJava:CookBook:PDB:Jmol" title="wikilink">How can I interact with

Jmol?</a></li>

<li><a href="BioJava:CookBook:PDB:hibernate" title="wikilink">How can I serialize to a

database?</a></li>

<h3 id="ontologies">Ontologies</h3>

<li><a href="BioJava:CookBook:OBO:parse" title="wikilink">How can I parse an OBO

file?</a></li>

<li><a href="BioJava:CookBook:OBO:visualize" title="wikilink">How can I visualize an OBO file as a directed acyclic

graph?</a></li>

<h3 id="cloud-computing">Cloud computing</h3>

<li><a href="BioJava:CookBook:Cloud:ec2" title="wikilink">How do I use Biojava in the Amazon EC2

cloud?</a></li>

<h2 id="disclaimer">Disclaimer</h2>

<p>This code is generously donated by people who probably have better

things to do. Where possible we test it but errors may have crept in. As

such, all code and advice here in has no warranty or guarantee of any

sort. You didn’t pay for it and if you use it we are not responsible for

anything that goes wrong. Be a good programmer and test it yourself

before unleashing it on your corporate database.</p>

<h2 id="copyright">Copyright</h2>

<p>The documentation on this site is the property of the people who

contributed it. If you wish to use it in a publication please make a

request through the <a href="&#109;&#097;&#105;&#108;&#116;&#111;:&#098;&#105;&#111;&#106;&#097;&#118;&#097;&#045;&#108;&#064;&#098;&#105;&#111;&#106;&#097;&#118;&#097;&#046;&#111;&#114;&#103;">biojava mailing

list</a>.</p>

<p>The code is <a href="wp:Open source" title="wikilink">open-source</a>. A good definition

of open-source can be found <a href="http://www.opensource.org/docs/osd">here</a>.

If you agree with that definition then you can use it.</p>

<p>–<a href="User:Guedes" title="wikilink">Guedes</a> 16:19, 28 March 2006 (EST)</p>