Name

Contents

Licence

Package

[http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html Genbank]

Public sequences

Publicly available

[http://bips.u-strasbg.fr/fr/Products/Databases/BAliBASE3/ BAliBASE3]

Sequence aligments version3, and a c program for scoring

unknown, but contains a header file from clustalw, which is not free

[http://www.compbio.dundee.ac.uk/Software/Oxbench/oxbench.html OXbench]

Multiple alignments and scoring system

[http://www.pseudogene.org www.pseudogene.org]

pseudogenes

unknown

[http://jaspar.genereg.net/ Jaspar]

Transcription factor bindng sites

"Freely available"

[http://www.bcgsc.ca:8080/oregano/Index.jsp ORegAnno]

Regulatory sequences

LGPL

[http://www.pazar.info Pazar]

public repository for regulatory data

Says Open Source but not found

[http://rebase.neb.com REbase]

Restriction Enzymes

?

[http://pdb.finkproject.org/pdb/package.php/embossdb-rebase fink]

[http://www.girinst.org/repbase/index.html Repbase]

Repeat elements

Academic, registration needed

[http://www.genetics.wustl.edu/fish_lab/repeats Zebrafish repeats]

Repeat elements (Zebrafish)

no license

Probably, many free databases can be found in the database issue of Nucleic Acid Research http://nar.oxfordjournals.org/content/vol34/suppl_1/index.dtl

We also need open-source software to warehouse the databases

Name

Licence

Package

Listed on microbio.wml?

[http://www.biomart.org/ ?BioMart]

LGPL

packaged ([http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/martj/ unofficial])

yes

[https://sourceforge.net/project/showfiles.php?group_id=147980 S3DB]

GPL

depends on PHP and (My|Postgre)SQL

no

[http://biomoby.open-bio.org/ BioMOBY]

Artistic

depends on java

no

[http://bioinformatics.ai.sri.com/biowarehouse/ ?BioWarehouse]

MPL 1.1

no


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