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Jose Manuel Duarte
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Updating to biojava 4
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‎wiki/BioJava:CookBook4.0.md‎

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title: BioJava:CookBook4.0
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---
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BioJava Cookbook for release 3.\*
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BioJava Cookbook for release 4.\*
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---------------------------------
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BioJava 3 is a major re-write of BioJava 1. As such many things work
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BioJava 3+ is a major re-write of BioJava 1. As such many things work
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differently. This cookbook provides examples how to work with the new
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codebase.
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Tutorial
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--------
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Many topics are also covered in the [BioJava 3
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tutorial](https://github.com/biojava/biojava3-tutorial).
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Many topics are also covered in the [BioJava
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tutorial](https://github.com/biojava/biojava-tutorial).
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How Do I....?
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-------------
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### Core Module - Working with Sequences
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**Required modules**: *biojava3-core*
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**Required modules**: *biojava-core*
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- [Overview of
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biojava3-core?](BioJava:CookBook:Core:Overview "wikilink")
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biojava-core?](BioJava:CookBook:Core:Overview "wikilink")
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- [How are sequences
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created?](BioJava:CookBook:Core:Sequences "wikilink")
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- [How do I compare two DNA Sequences and create a consensus
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### Protein Structure
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**Required modules**: *biojava3-structure, biojava3-alignment*
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**Optional module** : *biojava3-structure-gui* for the 3D visualisation
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**Optional external library** : *JmolApplet.jar* for the 3D
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visualisation
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**Required modules**: *biojava-structure, biojava-alignment* **Optional
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module** : *biojava-structure-gui* for the 3D visualisation **Optional
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external library** : *JmolApplet.jar* for the 3D visualisation
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- [How can I parse a PDB
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file?](BioJava:CookBook:PDB:read3.0 "wikilink")
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### Pairwise and Multiple Sequence Alignment
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**Required modules**: *biojava3-alignment, biojava3-core,
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biojava3-phylo* **Required external library**: *forester.jar*
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**Required modules**: *biojava-alignment, biojava-core, biojava-phylo*
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**Required external library**: *forester.jar*
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- [How can I read a Sequence Alignment in Stockholm
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format](BioJava:CookBook3:Stockholm "wikilink")? (Pfam, Rfam)
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### Genome
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**Required modules**: *biojava3-genome*
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**Required modules**: *biojava-genome*
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- [Overview of
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biojava3-genome?](BioJava:CookBook:genome:Overview "wikilink")
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### Sequencing
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**Required modules**: *biojava3-core*,*biojava3-sequencing* **Required
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**Required modules**: *biojava-core*,*biojava-sequencing* **Required
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external library**: *guava-11.0.1.jar*
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- [How do I work with nextgen sequencing reads in FASTQ
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format?](Biojava:CookBook3:FASTQ "wikilink")
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### Phylogenetic tree
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**Required modules**: ''biojava3-core **Required external library**:
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**Required modules**: ''biojava-core **Required external library**:
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*forester.jar*
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- [Overview of
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biojava3-phylo?](BioJava:CookBook:Phylo:Overview "wikilink")
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biojava-phylo?](BioJava:CookBook:Phylo:Overview "wikilink")
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<!-- -->
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### Physico-Chemical Properties Computation
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**Required modules**: *biojava3-aa-prop, biojava3-structure and
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biojava3-core*
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**Required modules**: *biojava-aa-prop, biojava-structure and
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biojava-core*
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- [How can I compute physico-chemical properties via
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### Protein Disorder
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**Required modules**: *biojava3-protein-disorder*
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**Required modules**: *biojava-protein-disorder*
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- [How can I predict disordered regions of the protein using its
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### Protein Modification Identification
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**Required modules**: *biojava3-modfinder, biojava-structure*
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**Required modules**: *biojava-modfinder, biojava-structure*
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- [How can I identify protein modifications in a 3D
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### Remote Web Service Calls
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**Required modules**: *biojava3-core, biojava-ws*
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**Required modules**: *biojava-core, biojava-ws*
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- [How can I use NCBI's QBlast service
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‎wiki/BioJava:CookBook4.0.mediawiki‎

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== BioJava Cookbook for release 3.*==
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== BioJava Cookbook for release 4.*==
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BioJava 3 is a major re-write of BioJava 1. As such many things work differently. This cookbook provides examples how to work with the new codebase.
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BioJava 3+ is a major re-write of BioJava 1. As such many things work differently. This cookbook provides examples how to work with the new codebase.
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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.
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== Tutorial ==
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Many topics are also covered in the [https://github.com/biojava/biojava3-tutorial BioJava 3 tutorial].
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Many topics are also covered in the [https://github.com/biojava/biojava-tutorial BioJava tutorial].
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== How Do I....? ==
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=== Core Module - Working with Sequences ===
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'''Required modules''': ''biojava3-core''
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* [[BioJava:CookBook:Core:Overview|Overview of biojava3-core?]]
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'''Required modules''': ''biojava-core''
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* [[BioJava:CookBook:Core:Overview|Overview of biojava-core?]]
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* [[BioJava:CookBook:Core:Sequences|How are sequences created?]]
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* [[BioJava:CookBook:Core:SequenceCompare|How do I compare two DNA Sequences and create a consensus sequence?]]
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* [[BioJava:CookBook:Core:FastaReadWrite|How do I read or write Fasta files?]]
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=== Protein Structure ===
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'''Required modules''': ''biojava3-structure, biojava3-alignment''
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'''Optional module''' : ''biojava3-structure-gui'' for the 3D visualisation
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'''Required modules''': ''biojava-structure, biojava-alignment''
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'''Optional module''' : ''biojava-structure-gui'' for the 3D visualisation
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'''Optional external library''' : ''JmolApplet.jar'' for the 3D visualisation
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* [[BioJava:CookBook:PDB:read3.0|How can I parse a PDB file?]]
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=== Pairwise and Multiple Sequence Alignment ===
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'''Required modules''': ''biojava3-alignment, biojava3-core, biojava3-phylo''
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'''Required modules''': ''biojava-alignment, biojava-core, biojava-phylo''
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'''Required external library''': ''forester.jar''
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* [[BioJava:CookBook3:Stockholm|How can I read a Sequence Alignment in Stockholm format]]? (Pfam, Rfam)
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* [[BioJava:CookBook3:MSAProfiler|How can I profile the time and memory requirements of a Multiple Sequence Alignment]]?
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=== Genome ===
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'''Required modules''': ''biojava3-genome''
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'''Required modules''': ''biojava-genome''
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* [[BioJava:CookBook:genome:Overview|Overview of biojava3-genome?]]
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=== Sequencing ===
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'''Required modules''': ''biojava3-core'',''biojava3-sequencing''
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'''Required modules''': ''biojava-core'',''biojava-sequencing''
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'''Required external library''': ''guava-11.0.1.jar''
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* [[Biojava:CookBook3:FASTQ|How do I work with nextgen sequencing reads in FASTQ format?]]
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=== Phylogenetic tree ===
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'''Required modules''': ''biojava-core
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* [[BioJava:CookBook:Phylo:Overview|Overview of biojava3-phylo?]]
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* [[BioJava:CookBook:Phylo:Overview|Overview of biojava-phylo?]]
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*[[BioJava:CookBook:Phylo:ProfileToMSA|How do I convert Profile object into Multiple Sequence Alignment object to be use in the TreeConstructor]]
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=== Physico-Chemical Properties Computation ===
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'''Required modules''': ''biojava3-aa-prop, biojava3-structure and biojava3-core''
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'''Required modules''': ''biojava-aa-prop, biojava-structure and biojava-core''
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* [[BioJava:CookBook:AAPROP:main|How can I compute physico-chemical properties via APIs?]]
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* [[BioJava:CookBook:AAPROP:commandprompt|How can I compute physico-chemical properties using Command Prompt?]]
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* [[BioJava:CookBook:AAPROP:profeat|How can I compute PROFEAT properties via APIs?]]
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=== Protein Disorder ===
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'''Required modules''': ''biojava3-protein-disorder''
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'''Required modules''': ''biojava-protein-disorder''
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* [[BioJava:CookBook3:ProteinDisorder|How can I predict disordered regions of the protein using its sequence?]]
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* [[BioJava:CookBook3:ProteinDisorderCLI|Can I use the predictor from the command line?]]
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=== Protein Modification Identification ===
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'''Required modules''': ''biojava3-modfinder, biojava-structure''
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'''Required modules''': ''biojava-modfinder, biojava-structure''
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* [[BioJava:CookBook3:ModFinder|How can I identify protein modifications in a 3D structure?]]
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* [[BioJava:CookBook3:SupportedProtMod|How can I get the list of supported protein modifications?]]
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* [[BioJava:CookBook3:AddProtMod|How can I define and register a new protein modification?]]
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=== Remote Web Service Calls ===
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'''Required modules''': ''biojava3-core, biojava-ws''
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'''Required modules''': ''biojava-core, biojava-ws''
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* [[BioJava:CookBook3:NCBIQBlastService|How can I use NCBI's QBlast service ?]]
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* [[BioJava:CookBook3:ParsingBlastXMLOutput|How can I use Blast XML Output in my program?]]

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