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Revision 12 as of 2006-07-08 13:56:22
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Comment: benchmark alignments database
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||[http://bips.u-strasbg.fr/fr/Products/Databases/BAliBASE2/ BAliBASE2]||Sequence aligments version2, and a c program for scoring||unknown|| ||

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/BAliBASE/ BAliBASE]

Sequence aligments and a c program for scoring

unknown

[http://bips.u-strasbg.fr/fr/Products/Databases/BAliBASE2/ BAliBASE2]

Sequence aligments version2, and a c program for scoring

unknown

[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://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

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

MPL 1.1


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