An Alternative To Alamut ?
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Entering edit mode
10.5 years ago
Katsubio ▴ 90

Hi all,

Is there a BioConductor or Perl package which can be an alternative to AlaMut ? What do you use for mutations detections ?

Thanks.

M

mutation • 3.2k views
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3
Entering edit mode

Some advice to improve your question: Ask the question based on the concrete analytical problem and the data you are having. It's difficult to evaluate a commercial software if you don't have it. It's harder, to find an open source package as a replacement. Especially something that promises you 'everything'. The product's description page is 'lofty' to sya the least... I can think about many tools for variation detection and data-integration. Like this, your question cannot be answered, if you give us a concrete example we maybe can help.

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Entering edit mode
10.5 years ago
User 59 13k

I'm not aware of anything in BioConductor or Perl packages that has this functionality, however it is the kind of package that has functionality similar to SIFT or PolyPhen2 - 'Pathogenic or Not' tools. It is perfectly possible to script access to these in Perl with WWW::Mechanize. I had a student recently working on this, the diagnostics lab in question was using AlaMut.

You might also want to look at AlignGVGD, MAPP, PMut, SNPs&GO although I'm not sure off the top of my head if any of these have a web-services interface rather than just a web interface.

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