imported>Deltaspace42: −Category:Bioinformatics software; +Category:Software using the GNU Lesser General Public License; ±Category:Java platform software→Category:Java (programming language) libraries using HotCat

2025-12-23T19:28:09Z

−Category:Bioinformatics software; +Category:Software using the GNU Lesser General Public License; ±Category:Java platform software→Category:Java (programming language) libraries using HotCat

← Previous revision		Revision as of 19:28, 23 December 2025
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	===Core Module===		===Core Module===
	This module provides Java [[Class (~~computer~~ programming)\|classes]] to model [[amino acid]] or [[nucleotide]] sequences. The classes were designed so that the names are familiar and make sense to biologists and also provide a concrete representation of the steps in going from a gene sequence to a protein sequence for computer scientists and programmers.		This module provides Java [[Class (programming)\|classes]] to model [[amino acid]] or [[nucleotide]] sequences. The classes were designed so that the names are familiar and make sense to biologists and also provide a concrete representation of the steps in going from a gene sequence to a protein sequence for computer scientists and programmers.

	A major change between the legacy BioJava project and BioJava3 lies in the way framework has been designed to exploit then-new innovations in Java. A sequence is defined as a generic [[Interface (computing)#Software interfaces in object-oriented languages\|interface]] allowing the rest of the modules to create any utility that operates on all sequences. Specific classes for common sequences such as DNA and proteins have been defined in order to improve usability for biologists. The translation engine really leverages this work by allowing conversions between DNA, RNA and amino acid sequences. This engine can handle details such as choosing the codon table, converting start codons to methionine, trimming stop codons, specifying the reading frame and handing ambiguous sequences.		A major change between the legacy BioJava project and BioJava3 lies in the way framework has been designed to exploit then-new innovations in Java. A sequence is defined as a generic [[Interface (computing)#Software interfaces in object-oriented languages\|interface]] allowing the rest of the modules to create any utility that operates on all sequences. Specific classes for common sequences such as DNA and proteins have been defined in order to improve usability for biologists. The translation engine really leverages this work by allowing conversions between DNA, RNA and amino acid sequences. This engine can handle details such as choosing the codon table, converting start codons to methionine, trimming stop codons, specifying the reading frame and handing ambiguous sequences.
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	* FATCAT algorithm for flexible and rigid body alignment.<ref name=fatcat>{{cite journal \|vauthors=Ye Y, Godzik A \|title=Flexible structure alignment by chaining aligned fragment pairs allowing twists \|journal=Bioinformatics \|volume=19 \|issue=Suppl 2\|pages=ii246–55 \|date=October 2003 \|pmid=14534198 \|doi=10.1093/bioinformatics/btg1086\|doi-access=free }}</ref>		* FATCAT algorithm for flexible and rigid body alignment.<ref name=fatcat>{{cite journal \|vauthors=Ye Y, Godzik A \|title=Flexible structure alignment by chaining aligned fragment pairs allowing twists \|journal=Bioinformatics \|volume=19 \|issue=Suppl 2\|pages=ii246–55 \|date=October 2003 \|pmid=14534198 \|doi=10.1093/bioinformatics/btg1086\|doi-access=free }}</ref>
	* The standard Combinatorial Extension (CE) algorithm.<ref>{{cite journal \|vauthors=Shindyalov IN, Bourne PE \|title=Protein structure alignment by incremental combinatorial extension (CE) of the optimal path \|journal=Protein Eng. \|volume=11 \|issue=9 \|pages=739–47 \|date=September 1998 \|pmid=9796821 \|doi=10.1093/protein/11.9.739\|doi-access=free }}</ref>		* The standard Combinatorial Extension (CE) algorithm.<ref>{{cite journal \|vauthors=Shindyalov IN, Bourne PE \|title=Protein structure alignment by incremental combinatorial extension (CE) of the optimal path \|journal=Protein Eng. \|volume=11 \|issue=9 \|pages=739–47 \|date=September 1998 \|pmid=9796821 \|doi=10.1093/protein/11.9.739\|doi-access=free }}</ref>
	* A new version of CE that can detect circular permutations in proteins.<ref>{{cite journal \|vauthors=Bliven S, Prlić A \|title=Circular permutation in proteins \|journal=PLOS Comput. Biol. \|volume=8 \|issue=3 \|~~pages~~=e1002445 \|year=2012 \|pmid=22496628 \|pmc=3320104 \|doi=10.1371/journal.pcbi.1002445 \|bibcode=2012PLSCB...8E2445B \|doi-access=free }}</ref>		* A new version of CE that can detect circular permutations in proteins.<ref>{{cite journal \|vauthors=Bliven S, Prlić A \|title=Circular permutation in proteins \|journal=PLOS Comput. Biol. \|volume=8 \|issue=3 \|article-number=e1002445 \|year=2012 \|pmid=22496628 \|pmc=3320104 \|doi=10.1371/journal.pcbi.1002445 \|bibcode=2012PLSCB...8E2445B \|doi-access=free }}</ref>
	These algorithms are used to provide the RCSB Protein Data Bank (PDB)<ref>{{cite journal \|vauthors=Rose PW, Beran B, Bi C \|title=The RCSB Protein Data Bank: redesigned web site and web services \|journal=Nucleic Acids Res. \|volume=39 \|issue=Database issue \|pages=D392–401 \|date=January 2011 \|pmid=21036868 \|pmc=3013649 \|doi=10.1093/nar/gkq1021 \|url=\|display-authors=etal}}</ref> Protein Comparison Tool as well as systematic comparisons of all proteins in the PDB on a weekly basis.<ref>{{cite journal \|vauthors=Prlić A, Bliven S, Rose PW \|title=Pre-calculated protein structure alignments at the RCSB PDB website \|journal=Bioinformatics \|volume=26 \|issue=23 \|pages=2983–5 \|date=December 2010 \|pmid=20937596 \|pmc=3003546 \|doi=10.1093/bioinformatics/btq572 \|url=\|display-authors=etal}}</ref>		These algorithms are used to provide the RCSB Protein Data Bank (PDB)<ref>{{cite journal \|vauthors=Rose PW, Beran B, Bi C \|title=The RCSB Protein Data Bank: redesigned web site and web services \|journal=Nucleic Acids Res. \|volume=39 \|issue=Database issue \|pages=D392–401 \|date=January 2011 \|pmid=21036868 \|pmc=3013649 \|doi=10.1093/nar/gkq1021 \|url=\|display-authors=etal}}</ref> Protein Comparison Tool as well as systematic comparisons of all proteins in the PDB on a weekly basis.<ref>{{cite journal \|vauthors=Prlić A, Bliven S, Rose PW \|title=Pre-calculated protein structure alignments at the RCSB PDB website \|journal=Bioinformatics \|volume=26 \|issue=23 \|pages=2983–5 \|date=December 2010 \|pmid=20937596 \|pmc=3003546 \|doi=10.1093/bioinformatics/btq572 \|url=\|display-authors=etal}}</ref>

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	In general, for small programs (<500 lines) that will be used by only an individual or small group, it is hard to beat [[Perl]] and [[BioPerl]]. These constraints probably cover the needs of 90 per cent of personal bioinformatics programming.		In general, for small programs (<500 lines) that will be used by only an individual or small group, it is hard to beat [[Perl]] and [[BioPerl]]. These constraints probably cover the needs of 90 per cent of personal bioinformatics programming.

	For beginners, and for writing larger programs in the Bio domain, especially those to be shared and supported by others, [[Python (programming language)\|~~Python’s~~]] clarity and brevity make it very attractive.		For beginners, and for writing larger programs in the Bio domain, especially those to be shared and supported by others, [[Python (programming language)\|Python's]] clarity and brevity make it very attractive.

	For those who might be leaning towards a career in bioinformatics and who want to learn only one language, [[Java (programming language)\|Java]] has the widest general programming support, very good support in the Bio domain with BioJava, and is now the de facto language of business (the new COBOL, for better or worse).		For those who might be leaning towards a career in bioinformatics and who want to learn only one language, [[Java (programming language)\|Java]] has the widest general programming support, very good support in the Bio domain with BioJava, and is now the de facto language of business (the new COBOL, for better or worse).
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	* [http://raphaelbauer.github.io/lajolla/ LaJolla]: An open source [[structural alignment]] tool for RNA and proteins using an index structure for fast alignment of thousands of structures; includes an easy-to-use command line interface.		* [http://raphaelbauer.github.io/lajolla/ LaJolla]: An open source [[structural alignment]] tool for RNA and proteins using an index structure for fast alignment of thousands of structures; includes an easy-to-use command line interface.
	* [http://www.genbeans.org/ GenBeans]: A rich client platform for bioinformatics primarily focused on molecular biology and sequence analysis.		* [http://www.genbeans.org/ GenBeans]: A rich client platform for bioinformatics primarily focused on molecular biology and sequence analysis.
	* [~~http~~://jensembl.sourceforge.net/ JEnsembl]: A version-aware Java API to Ensembl data systems.<ref>{{cite journal\|vauthors=Paterson T, Law A\|date=November 2012\|title=JEnsembl: a version-aware Java API to Ensembl data systems\|url= \|journal=Bioinformatics\|volume=28\|issue=21\|pages=2724–31\|doi=10.1093/bioinformatics/bts525\|pmc=3476335\|pmid=22945789}}</ref>		* [https://jensembl.sourceforge.net/ JEnsembl]: A version-aware Java API to Ensembl data systems.<ref>{{cite journal\|vauthors=Paterson T, Law A\|date=November 2012\|title=JEnsembl: a version-aware Java API to Ensembl data systems\|url= \|journal=Bioinformatics\|volume=28\|issue=21\|pages=2724–31\|doi=10.1093/bioinformatics/bts525\|pmc=3476335\|pmid=22945789}}</ref>
	* [https://www.kimlab.org/software/musi MUSI]: An integrated system to identify multiple specificity from very large peptide or nucleic acid data sets.<ref>{{cite journal\|display-authors=etal\|vauthors=Kim T, Tyndel MS, Huang H\|date=March 2012\|title=MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets\|url= \|journal=Nucleic Acids Res.\|volume=40\|issue=6\|pages=e47\|doi=10.1093/nar/gkr1294\|pmc=3315295\|pmid=22210894}}</ref>		* [https://www.kimlab.org/software/musi MUSI]: An integrated system to identify multiple specificity from very large peptide or nucleic acid data sets.<ref>{{cite journal\|display-authors=etal\|vauthors=Kim T, Tyndel MS, Huang H\|date=March 2012\|title=MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets\|url= \|journal=Nucleic Acids Res.\|volume=40\|issue=6\|pages=e47\|doi=10.1093/nar/gkr1294\|pmc=3315295\|pmid=22210894}}</ref>
	* [https://www.mdpi.com/2218-273X/10/3/461 Bioshell]: A utility library for structural bioinformatics<ref>{{cite journal\|vauthors=Gront D, Kolinski A\|date=February 2008\|title=Utility library for structural bioinformatics\|journal=Bioinformatics\|volume=24\|issue=4\|pages=584–5\|doi=10.1093/bioinformatics/btm627\|pmid=18227118\|doi-access=free}}</ref>		* [https://www.mdpi.com/2218-273X/10/3/461 Bioshell]: A utility library for structural bioinformatics<ref>{{cite journal\|vauthors=Gront D, Kolinski A\|date=February 2008\|title=Utility library for structural bioinformatics\|journal=Bioinformatics\|volume=24\|issue=4\|pages=584–5\|doi=10.1093/bioinformatics/btm627\|pmid=18227118\|doi-access=free}}</ref>
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	* {{Official website}}		* {{Official website}}

	~~[[Category:Bioinformatics software]]~~		[[Category:Java (programming language) libraries]]
	[[Category:Java ~~platform software~~]]
	[[Category:Free bioinformatics software]]		[[Category:Free bioinformatics software]]
			[[Category:Software using the GNU Lesser General Public License]]

240B:C020:424:2E6A:0:30:4E3F:3F01 at 10:35, 19 March 2025

2025-03-19T10:35:27Z

Show changes

BioJava - Revision history

imported>Deltaspace42: −Category:Bioinformatics software; +Category:Software using the GNU Lesser General Public License; ±Category:Java platform software→Category:Java (programming language) libraries using HotCat

240B:C020:424:2E6A:0:30:4E3F:3F01 at 10:35, 19 March 2025