Question

An Alternative To Alamut ?

4

Entering edit mode

13.6 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 • 4.3k views

ADD COMMENT • link updated 13.6 years ago by User 59 13k • written 13.6 years ago by Katsubio ▴ 90

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.

ADD REPLY • link 13.6 years ago by Michael 54k

score 5 · Answer 1 · 2010-10-06

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.