<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>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.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Borhan, Hossein" <<a href="mailto:Hossein.Borhan@AGR.GC.CA">Hossein.Borhan@AGR.GC.CA</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 13 March, 2013 5:49 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] do of the maker predicted proteins do not start with M<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; "><div><div><div style="font-family: Calibri, sans-serif; "><span class="Apple-style-span" style="font-family: Calibri; "><div style="font-family: Calibri, sans-serif; ">Hi </div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; ">I have run maker and some of the protein predicted by maker does not start with a Methionine. I am not sure why</div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; ">Here are some examples</div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><div>>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</div><div>VIIKFKTFAKASRSVELFGHEGAWARGDGYCNFKTESEKADRSVKSSCSLNIPFTYDVGR</div><div>RQYVIKGDRFCLSHNHLVMIPSPTTVIVNDQRDLTPDQLSYIINLGKYSLPFPMVTRMLS</div><div>DQFPDCRIQKPLLHRLLRKGKLQAFGGDRDAMNALINLGRSYEEHGGFFEIDIDVDCRLE</div><div>KIWLARAEGLQFASVYNDVVQIDGGAKMNAYGFVFLPVTVIDCLGKSYVVGAMAGPSAEN</div><div>KADVVKTLEYFRVKRSESVLIADDALAFRAAAVECDMVYHQCTKHYQAKIARACAGLGHE</div><div>GKEFMIKANTLVYHIFPSEDAFFAKADEYRLMFLQYGGAVKLFDDIVDKRQQLCRTFTSC</div><div>KFTGSHSSNQRAEGTISRTKRDVQPWLSRANLFEMFTHLEMIQKQQEDEAARLLSNLIRK</div><div>GKHWSDYVDSIFRERQLNSRLLSSVREVDTGLH</div></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><div>>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</div><div>ALSLHGTRQAFARVPPPCRRAHPAERRQPGGGMSADAPVKAGYLLKLTSSLSHWNRRYFI</div><div>VADTKLFYCKTEDDLLRRKFQGEIDLAGAQIALYTRNDETAKRFSDHHHMLGVKPAGCDR</div><div>IYILDADSEHAQKEWVACLRRHASQAPVSSPVDAAVAAAPRKDPQSVREGFLTKRGETIK</div><div>NWKMRYFVLKGNYLHYYRSIEDAQPAGSILLLGTRTTAEPKAVTGMPHSFSIARADAKRK</div><div>YMIHADSKEECDAWVGAIQQQSVFVRHAGTDSAPPEVVAPAAATPVHQQHQSRSSFGNRP</div><div>NVADDSADDDEAALDEVALSNGPPALAPHGIANTGASTGLNLKQKVSKKKRRFVTDEFDL</div><div>DLTYITENIIAMGFPAESMEAMFRNSMSDVQRFLDGRHPDAYRVYNLCSERDYDPAKFHH</div><div>NVCRFPFDDHNCPNFEDLIPLCEDIHNWLSIQSDHVVAIHCKAGKGRTGLVICAYLLYSG</div><div>AWRTARDALQFYGFVRTQDQKGVTIPSQIRYVEYFEQYMADPEILSRNNGPLVISEIFVG</div><div>RGCRPFDTVTITNMGRRMNSKDWGKYWKDALDDGLLLQLPKGACQVDKDFKVEFLASGLL</div><div>GKKTRVAGFWLHTAFIQDGVVDIDKSMIDKVNKEKDCPAFSIQVFFGGRTYVDRRCRIPV</div><div>APPQPTGPLLLSPATVRIRNADPLPVPNPSSPSESPSFSAMSSVPSLSLESLSSVSSSLS</div><div>PTTGPKAAPSPKKQDPGLDPGSPPGTVKSAPVAEAGAAPVDARSDNKAPARSCSLPHGRF</div><div>PGDVAGDGAFQQAAVQVRIAFWNNLQSEALQRRNSRL</div></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><div>>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</div><div>STSTVFCPGLWNRVGRYVSGGLQTSPVTVPRQVRPICLATQPATDQPGYVMSSTSALVGI</div><div>GVVTVALLCRWAPILVTTSGPGSPARSSADVMRIWADHDWSAGTTSLPISQESLLAKRVL</div><div>SKSFDGLPPNLHVQDDTVPVALLRAHLNAGRHMRLRDMCPTAGACDLQGADPDHGLAPLH</div><div>MAAMRDDRSSIAYLMALGADPDAMDRAGRQYRNLSFTNFVRNARRAAEERGSTCQLPEVN</div><div>LAGLERADLDRSWAEIRRLAHEGEPVAIRGLLGAYDRSDVLDWDLDAFLTRHGHVPVNVG</div><div>DVPYAQYFGLPIQSMPLSKYVASLAPGSASYVFAKDDGICRDALQILDRFARDALPPYFV</div><div>SPAALGSDAVHFYLGNKGSGAPFHLHSDAVNLLAHGSKTWFVTPPPQSVYSRTPIGEFAA</div><div>NGTSGIESLRCEQNPGDAIYIPFDWGHAVLNNEDSTFGFAVELLNKRDSLHFLRPSSQVP</div><div>AGQ</div></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; ">Regards</div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; ">Hossein</div></span></div><div><div style="color: rgb(0, 0, 0); font-size: 14px; "><br></div><div style="font-family: Calibri, sans-serif; "><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 14px; color: rgb(0, 0, 0); margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; "><font class="Apple-style-span" face="Arial,sans-serif"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 14px; color: rgb(0, 0, 0); margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; "><font class="Apple-style-span" face="Arial,sans-serif"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 14px; color: rgb(0, 0, 0); margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; "><font class="Apple-style-span" face="Arial,sans-serif"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></p></div></div></div></div></div></div>
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