Changing the genetic code table in MAKER

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Changing the genetic code table in MAKER

Yu-Hsuan Cheng
Hi,

This is YuHsuan Cheng, who is a PhD student from Taiwan. I want to use the MAKER combining with SNAP to annotate ciliates genome. The genetic code for ciliates is different from other species, so I am wondering that if there is any option in MAKER I can change the genetic code table? I also asked Dr. Korf about this issue, he said SNAP has no way to change the genetic code table. I will use Augustus combining with Maker later on. 
The pipeline I used previously is as followed.
1. MAKER (Hints from proteome and RNAseq)
2. MAKER to Zff  
3. ~/bin/maker/exe/snap/hmm-assembler.pl snapFirst . > ../../snapFirst.hmm
and then used snapFirst.hmm as hints in MAKER

Look forward to your reply. Thank you.

Best wishes,

YuHsuan 

Yu-Hsuan Cheng 鄭毓鋗
Institute of Molecular Biology
Academia Sinica
128 Academia road, Section 2
Nankang, Taipei 115
Taiwan
Phone:<a href="tel:+886%202%202789%209216" value="+886227899216" target="_blank">+886-2-2789-9216 (Lab), <a href="tel:+886%20958%20216%20538" value="+886958216538" target="_blank">+886-958-216-538 (Mobile phone)

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Re: Changing the genetic code table in MAKER

Carson Holt-2
Sorry. MAKER does not currently support alternate codon tables.

—Carson


On Nov 30, 2017, at 11:20 PM, Yu-Hsuan Cheng <[hidden email]> wrote:

Hi,

This is YuHsuan Cheng, who is a PhD student from Taiwan. I want to use the MAKER combining with SNAP to annotate ciliates genome. The genetic code for ciliates is different from other species, so I am wondering that if there is any option in MAKER I can change the genetic code table? I also asked Dr. Korf about this issue, he said SNAP has no way to change the genetic code table. I will use Augustus combining with Maker later on. 
The pipeline I used previously is as followed.
1. MAKER (Hints from proteome and RNAseq)
2. MAKER to Zff  
3. ~/bin/maker/exe/snap/hmm-assembler.pl snapFirst . > ../../snapFirst.hmm
and then used snapFirst.hmm as hints in MAKER

Look forward to your reply. Thank you.

Best wishes,

YuHsuan 

Yu-Hsuan Cheng 鄭毓鋗
Institute of Molecular Biology
Academia Sinica
128 Academia road, Section 2
Nankang, Taipei 115
Taiwan
Phone:<a href="tel:+886%202%202789%209216" value="+886227899216" target="_blank" class="">+886-2-2789-9216 (Lab), <a href="tel:+886%20958%20216%20538" value="+886958216538" target="_blank" class="">+886-958-216-538 (Mobile phone)
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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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[hidden email]
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