Question

Is there an equivalent of Biopython for Java?

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8.7 years ago

onemoreuser ▴ 20

I would like to know if there is something like Entrez from Biopython for Java. I would like to access databases like dbSNP to collect data from different variants.

java biopython python databases • 2.4k views

ADD COMMENT • link updated 8.7 years ago by Pierre Lindenbaum 164k • written 8.7 years ago by onemoreuser ▴ 20

score 4 · Answer 1 · 2016-02-29

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8.7 years ago

Pierre Lindenbaum 164k

Biojava : http://biojava.org/wiki/Main_Page

to access dbsnp by rs##, you can always use NCBI eutils.... How To Get A Dbsnp Data From Java?

ADD COMMENT • link 8.7 years ago by Pierre Lindenbaum 164k

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I searched the Biojava page and the methods that I want to use are available in version 1.9 but I only find the .jar files for version 4.1.0.

ADD REPLY • link 8.7 years ago by onemoreuser ▴ 20

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If I recall correctly, not everything has been ported from the "legacy" BioJava codebase - I'm sure help would be welcome.

ADD REPLY • link 8.7 years ago by Peter 6.0k

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I tried to use NCBI eUtils but I don't get any output with that.

ADD REPLY • link 8.7 years ago by onemoreuser ▴ 20