[maker-devel] do of the maker predicted proteins do not start with M

[Carson Holt]

SNAP and other gene prediction programs are capable of producing partial
models if they can't find reasonable start and stop codons.  You can set
always_complete=1 in the maker_opts.ctl file to get MAKER to walk forward
and backwards to search for starts and stops after the ab initio predictors
do their work in an attempt to force model completion.

Thanks,
Carson



From:  "Borhan, Hossein" <Hossein.Borhan at AGR.GC.CA>
Date:  Wednesday, 13 March, 2013 5:49 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] do of the maker predicted proteins do not start with
M

Hi 

I have run maker and  some of the protein predicted by maker does not start
with a Methionine. I am not sure why

Here are some examples

>maker-scaffold00001-snap-gene-0.8-mRNA-1 protein AED:0.27496328928047
eAED:0.27496328928047 QI:0|0.4|0.16|0.5|1|1|6|0|453
VIIKFKTFAKASRSVELFGHEGAWARGDGYCNFKTESEKADRSVKSSCSLNIPFTYDVGR
RQYVIKGDRFCLSHNHLVMIPSPTTVIVNDQRDLTPDQLSYIINLGKYSLPFPMVTRMLS
DQFPDCRIQKPLLHRLLRKGKLQAFGGDRDAMNALINLGRSYEEHGGFFEIDIDVDCRLE
KIWLARAEGLQFASVYNDVVQIDGGAKMNAYGFVFLPVTVIDCLGKSYVVGAMAGPSAEN
KADVVKTLEYFRVKRSESVLIADDALAFRAAAVECDMVYHQCTKHYQAKIARACAGLGHE
GKEFMIKANTLVYHIFPSEDAFFAKADEYRLMFLQYGGAVKLFDDIVDKRQQLCRTFTSC
KFTGSHSSNQRAEGTISRTKRDVQPWLSRANLFEMFTHLEMIQKQQEDEAARLLSNLIRK
GKHWSDYVDSIFRERQLNSRLLSSVREVDTGLH

>snap-scaffold00087-abinit-gene-2.145-mRNA-1 protein AED:0.0539495114006514
eAED:0.0539495114006514 QI:2|1|0.6|1|1|1|5|0|817
ALSLHGTRQAFARVPPPCRRAHPAERRQPGGGMSADAPVKAGYLLKLTSSLSHWNRRYFI
VADTKLFYCKTEDDLLRRKFQGEIDLAGAQIALYTRNDETAKRFSDHHHMLGVKPAGCDR
IYILDADSEHAQKEWVACLRRHASQAPVSSPVDAAVAAAPRKDPQSVREGFLTKRGETIK
NWKMRYFVLKGNYLHYYRSIEDAQPAGSILLLGTRTTAEPKAVTGMPHSFSIARADAKRK
YMIHADSKEECDAWVGAIQQQSVFVRHAGTDSAPPEVVAPAAATPVHQQHQSRSSFGNRP
NVADDSADDDEAALDEVALSNGPPALAPHGIANTGASTGLNLKQKVSKKKRRFVTDEFDL
DLTYITENIIAMGFPAESMEAMFRNSMSDVQRFLDGRHPDAYRVYNLCSERDYDPAKFHH
NVCRFPFDDHNCPNFEDLIPLCEDIHNWLSIQSDHVVAIHCKAGKGRTGLVICAYLLYSG
AWRTARDALQFYGFVRTQDQKGVTIPSQIRYVEYFEQYMADPEILSRNNGPLVISEIFVG
RGCRPFDTVTITNMGRRMNSKDWGKYWKDALDDGLLLQLPKGACQVDKDFKVEFLASGLL
GKKTRVAGFWLHTAFIQDGVVDIDKSMIDKVNKEKDCPAFSIQVFFGGRTYVDRRCRIPV
APPQPTGPLLLSPATVRIRNADPLPVPNPSSPSESPSFSAMSSVPSLSLESLSSVSSSLS
PTTGPKAAPSPKKQDPGLDPGSPPGTVKSAPVAEAGAAPVDARSDNKAPARSCSLPHGRF
PGDVAGDGAFQQAAVQVRIAFWNNLQSEALQRRNSRL

>augustus-scaffold00087-abinit-gene-0.106-mRNA-1 protein AED:0.10935424621144
eAED:0.10935424621144 QI:1|1|0.66|1|1|1|3|0|483
STSTVFCPGLWNRVGRYVSGGLQTSPVTVPRQVRPICLATQPATDQPGYVMSSTSALVGI
GVVTVALLCRWAPILVTTSGPGSPARSSADVMRIWADHDWSAGTTSLPISQESLLAKRVL
SKSFDGLPPNLHVQDDTVPVALLRAHLNAGRHMRLRDMCPTAGACDLQGADPDHGLAPLH
MAAMRDDRSSIAYLMALGADPDAMDRAGRQYRNLSFTNFVRNARRAAEERGSTCQLPEVN
LAGLERADLDRSWAEIRRLAHEGEPVAIRGLLGAYDRSDVLDWDLDAFLTRHGHVPVNVG
DVPYAQYFGLPIQSMPLSKYVASLAPGSASYVFAKDDGICRDALQILDRFARDALPPYFV
SPAALGSDAVHFYLGNKGSGAPFHLHSDAVNLLAHGSKTWFVTPPPQSVYSRTPIGEFAA
NGTSGIESLRCEQNPGDAIYIPFDWGHAVLNNEDSTFGFAVELLNKRDSLHFLRPSSQVP
AGQ


Regards

Hossein






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