<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hello,<div class=""><br class=""></div><div class="">You have received these e-mails because you are subscribed to the Ensembl developers list. Subscribe/unsubscribe information can be found at the bottom of each e-mail.</div><div class=""><br class=""></div><div class="">Best wishes</div><div class=""><br class=""></div><div class="">Ben<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 17 Apr 2018, at 10:51, mawenlong <<a href="mailto:mawenlong_nwsuaf@163.com" class="">mawenlong_nwsuaf@163.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="line-height: 1.7; font-size: 14px; font-family: Arial;" class=""><div class="">Hi.</div><div class="">Recently, I kept receving your emails.</div><div class="">But, I have done nothing about this work.</div><div class="">So, is there any wrong message?<br class="">Best wish for your reaserch.</div><div style="position:relative;zoom:1" class=""></div><div id="divNeteaseMailCard" class=""></div><br class=""><pre class=""><br class="">At 2018-04-17 03:15:51, "David Mathog" <<a href="mailto:mathog@caltech.edu" class="">mathog@caltech.edu</a>> wrote:
>On 16-Apr-2018 06:46, Thibaut Hourlier wrote:
>> • Mask the genome using RepeatMasker and repbase. In some case we
>> would use repeatmodeler to create a repeat library
>
>NP_999661.1.fasta (NCBI predicted protein 3908aa)
>dystrophin_pep.fasta (evigene predicted protein, 3908aa,
> differs from preceding by 12 aa changes, no indels).
>Scaffold162.fasta (Sea urchin genome DNA for region, not masked)
>
>
>> • Align species specific data with exonerate/genewise
>
>Tried NP_999661 and Scaffold162 on the genewise web
>service with these results:
>
><a href="https://www.ebi.ac.uk/Tools/services/web_genewise/toolresult.ebi?jobId=genewise-E20180416-173516-0354-73422181-p2m&analysis=alignment" class="">https://www.ebi.ac.uk/Tools/services/web_genewise/toolresult.ebi?jobId=genewise-E20180416-173516-0354-73422181-p2m&analysis=alignment</a>
>
>The prediction is on the wrong strand. I don't see a way to set that.
>
>exonerate gives slightly different, and not so great, results with
>these two peptide sequences:
>
>exonerate --model protein2genome --percent 20 -q dystrophin_pep.fasta \
> -Q protein -T dna -t Scaffold162.fasta >/tmp/evigenePep_vs_genome.txt
>#maps 486-2794 402842-264692
>#maps 2798-2845 392816-392724 with 141348bp intron and then
>#maps 2846-3668 251325-193226
>
>So missing 485aa at the start, 4aa in the middle, 240aa at the end, plus
>a few aa inside the alignments. When run instead with NP_999661.1.fasta
>the first and last alignments are still found but the center one is not.
> If the missing pieces of the protein query are extracted and run
>separately more alignments are found, but exonerate doesn't map
>everything in one pass. The "--percent 20" came from Maker. If it is
>lowered to 2 from 20, or omitted, then NP_999661 maps like:
>
> 0 - 29 517984 - 517897
> 0 - 455 513283 - 404660
> 485 - 2794 402842 - 264691
>2845 - 3668 251324 - 193225
>3667 - 3835 186617 - 380919
>3749 - 3908 184419 - 181360
>
>and dystrophin_pep like:
> 0 - 29 517984 - 517897
> 0 - 455 513283 - 404660
> 485 - 2794 402842 - 264691
>2797 - 3668 392816 - 193225
>3667 - 3835 186617 - 380919
>3749 - 3908 184419 - 181360
>
>Which has things in more or less the right order, but it seems pretty
>confused about the 181k-392k region.
>
>> • Align protein from other species with genBlast
>
>Cheating here, using the same species, positive control...
>
>#downloaded genblastg, link "genblast" to it.
>ln -s /home/mathog/src/genblast/alignscore.txt alignscore.txt
>ln -s /home/mathog/bin/blastall blastall
>genblast -p genblastg -q NP_999661.1.fasta -t Scaffold162.fasta \
> -o myoutput -gff -id 58 -cdna -pro
>
>and
>
>genblast -p genblastg -q NP_999661.1.fasta -t Scaffold162.fasta \
> -o myoutput -gff -id 58 -cdna -pro
>
>Both have the same 3725aa peptide for the best prediction. See the
>attached dotplot to see which pieces are missing, which not surprisingly
>are somewhat correlated with the ends of the exonerate ranges. So far
>genblast has given the best non-NCBI mapping of this protein to the
>genome. Unfortunately it is still missing chunks here and there.
>Perhaps one of genblast's many parameters compensates for bad sequence
>and will put them back in?
>
>Thanks,
>
>David Mathog
><a href="mailto:mathog@caltech.edu" class="">mathog@caltech.edu</a>
>Manager, Sequence Analysis Facility, Biology Division, Caltech
</pre></div><br class=""><br class=""><span title="neteasefooter" class=""><div class=""> <br class="webkit-block-placeholder"></div></span>_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""><div class="">
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