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sam.predict-2nd for make_fragments.pl script

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sam.predict-2nd for make_fragments.pl script
#1

Hi

Could anyone tell me where to get predict-2nd software for membrane_abinitio application ? I am trying to run make_fragments.pl and it is asking for predict-2nd software. Could anyone please help me ?

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Thu, 2011-02-17 12:29
sumukh21
Thu, 2011-02-17 13:14
smlewis

Hi

I tried using this but it does not seems to have 'overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net' file. Instead it has 't2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-stride-seeded.net' file and the program make_fragments.pl saying 'sam.predict-2nd failed' . Could you help me in this matter ?

Thu, 2011-02-17 15:05
sumukh21

The 'overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net' file is found in:

http://users.soe.ucsc.edu/~karplus/predict-2nd/testing/stride/networks/

Thu, 2013-05-09 17:14
fukamitka