<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Emmanuel, <div class=""><br class=""></div><div class="">I can’t tell whether it’s will work from the blast lines that you sent. It will depend on the full headers in the fasta lines, which you’ll run after all the blasts are complete. </div><div class=""><br class=""></div><div class="">Assembly isn’t really my expertise or the topic of this mailing list, but assembling your contigs into scaffolds would probably help your annotations by connecting some parts of genes that are broken across contigs, and will definitely help downstream analysis if you need to know which genes are located next to each other. </div><div class=""><br class=""></div><div class="">How much improvement you can get by scaffolding depends on the type of sequence data you have. Each scaffolder makes assumptions and has requirements, and some assemblers like velvet and SOAPdenovo have scaffolding built into their algorithms. I’d recommend starting with a review like this one: <a href="http://www.sciencedirect.com/science/article/pii/S1672022912000095" class="">http://www.sciencedirect.com/science/article/pii/S1672022912000095</a></div><div class=""><br class=""></div><div class="">~Daniel</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 2, 2017, at 10:47 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello Daniel,<div class=""><br class=""></div><div class="">Thanks for the tip, I was able to download uniprot_swiss.fa I am currently running the blast now</div><div class=""><br class=""></div><div class="">it looks like this</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">MUCPR_041061-RA<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>sp|P10978|POLX_TOBAC<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>49.315<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>73<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>37<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>43<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>115<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>874<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>946<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>2.95e-14<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>71.6</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">MUCPR_026643-RA<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>sp|Q00451|PRF1_SOLLC<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>86.207<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>87<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>11<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>1<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>243<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>328<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>257<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>343<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>3.65e-32<span class="gmail-Apple-tab-span" style="white-space:pre"> </span>126</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">Is it ok?</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">I wish to ask, I did not assemble my contigs into scaffold before annotating would it affect the end result?</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">I wish to assemble my sequence into scaffold can you advice on the best software to use?</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">I attempted using <strong style="font-family: verdana, geneva, lucida, 'lucida grande', arial, helvetica, sans-serif;" class="">SSPACE: a new stand-alone scaffolding tool for small and large genomes</strong></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><strong style="font-family: verdana, geneva, lucida, 'lucida grande', arial, helvetica, sans-serif;" class="">but am having problem with the library. Funny enough the software does not have support to solve problems</strong></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><strong style="font-family: verdana, geneva, lucida, 'lucida grande', arial, helvetica, sans-serif;" class=""><br class=""></strong></div><div style="margin: 0px; font-size: 11px; line-height: normal;" class=""><font face="verdana, geneva, lucida, lucida grande, arial, helvetica, sans-serif" class=""><b class="">Thanks</b></font></div></div><div class=""><br class=""></div><div class=""><br class=""></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Mon, Oct 2, 2017 at 2:17 PM, Daniel Ence <span dir="ltr" class=""><<a href="mailto:dandence@gmail.com" target="_blank" class="">dandence@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi Emmanuel, I think this script is expecting the file “uniprot_sprot.fasta” downloaded from the uniprot download page at <font color="#4787ff" class=""><u class=""><a href="http://www.uniprot.org/downloads#uniprotkblink" target="_blank" class="">http://www.uniprot.org/<wbr class="">downloads#uniprotkblink</a></u></font><div class="">The fasta headers in this file are different from the fasta header that the file you used has: </div><div class=""><div style="margin:0px;font-size:11px;font-family:Menlo" class="">>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1</div><div style="margin:0px;font-size:11px;font-family:Menlo" class=""><br class=""></div><div style="margin:0px" class="">Let us know if that helps, </div><span class="HOEnZb"><font color="#888888" class=""><div style="margin:0px" class="">Daniel</div></font></span><div class=""><div class="h5"><div style="margin:0px;font-size:11px;font-family:Menlo" class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="">On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class="m_-3504412003310728126Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello,<div class="">I intend to rename genes for Genebank submission</div><div class=""><br class=""></div><div class="">I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. </div><div class=""><br class=""></div><div class="">the output of BLAST RESULT looks like this</div><div class=""><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">snap_masked-contig_8151-<wbr class="">processed-gene-0.8-mRNA-1 P10978.1 49.315 73 37 0 43 115 874 946 2.61e-14 71.6</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">I got the following result</span></div></div><div class=""><br class=""><div class=""><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/<wbr class="">Gpm/maker/bin/maker_<wbr class="">functional_gff line 139, <$IN> line 2897906.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/<wbr class="">Gpm/maker/bin/maker_<wbr class="">functional_gff line 141, <$IN> line 2897906.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/<wbr class="">Gpm/maker/bin/maker_<wbr class="">functional_gff line 139, <$IN> line 1608599.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/<wbr class="">Gpm/maker/bin/maker_<wbr class="">functional_gff line 141, <$IN> line 1608599.</span></div><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">
</span></p><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">What can I do?</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class=""><div class="m_-3504412003310728126gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/<wbr class="">publications</a></div></div></div></div>
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