Hi Ed and Suzanna, Thank you very much for your help!
As for FASTA file for the database, this Physcomitrella patens' sequence seems to me that there is a little evidence that this region might be a putative gene with the RRM domain. I used SIM4 output file and this query sequence mentioned above and let Apollo pass them with default parameters - I didn't remove any aligments with regard for their alignment length or alignment identity, I didn't limit SIM4 results at all. Why does Apollo display results from different analysises (FGENESH, GENSCAN, blastx, genemark.hmm) in this particular region, but discard those results from SIM4? Best regards, Andrzej On Fri, Nov 14, 2008 at 3:16 AM, Suzanna Lewis <[EMAIL PROTECTED]> wrote: > Hi Ed, > > I was just thinking that perhaps one thing we could also do is provide a > "parse" report at the end. Something along the lines of: xxx total > alignments parsed, nnn were acceptable. It could get fancier I suppose and > say why things were deemed bad alignments, but something to let the user > know that the work was done and what the results are, even in those cases > where 0 things aligned. > > -S > > > On Nov 13, 2008, at 4:33 PM, Ed Lee wrote: > > Hi Andrzej, >> >> Could you provide me with the FastA file for the database you used and >> the exact options you passed to sim4? The reason why the first sets of >> results are not displayed is because the intron orientations switch >> within the alignment (494-1132 / 1304-1718). Apollo disregards those >> alignments as they are rather suspect. >> >> Cheers, >> Ed >> >> On Thu, 2008-11-13 at 16:12 +0100, Andrzej Zielezinski wrote: >> >>> >>> >>> ---------- Forwarded message ---------- >>> From: Andrzej Zielezinski <[EMAIL PROTECTED]> >>> Date: Thu, Nov 13, 2008 at 4:10 PM >>> Subject: Loading data - computational analysis - SIM4 >>> To: [email protected] >>> >>> >>> Hello everyone, >>> >>> Firstly, Apollo is a great tool for genome annotation and for >>> gathering results from different analysises and I would like to thank >>> authors for a such helpful tool. >>> >>> There is one thing I can't cope with. When I load data from SIM4's >>> output file, I've noticed that some units of this loaded SIM4 feature >>> are missing in the Apollo main window. >>> >>> To be understood here I employed some example: >>> Results from SIM4 analysis: >>> >>> seq1 = genomic_dna.fasta, 3046 bp >>> seq2 = ests_ppatens.fasta.screen.cap.contigs (Contig1), 2058 bp >>> >>> 142-271 (194-323) 81% == >>> 494-1132 (396-1037) 83% <- >>> 1304-1718 (1038-1452) 81% -> >>> 1971-2053 (1453-1535) 90% >>> >>> seq1 = genomic_dna.fasta, 3046 bp >>> seq2 = ests_ppatens.fasta.screen.cap.contigs (Contig2), 841 bp >>> >>> (complement) >>> 1597-1718 (8-129) 84% -> >>> 1971-2053 (130-212) 90% >>> >>> When I load this file and query file also (with genomic sequence) >>> Apollo shows only two tiers: 1597-1718 (8-129) 84% -> and 1971-2053 >>> (130-212) 90%. What has be-come of other elements that should have >>> been shown? >>> >>> Above mentioned situation happens with different SIM4's results. >>> >>> Thank you in advance! >>> >>> Kindest regards, >>> Andrzej Zielezinski >>> >>> _______________________________________________ >>> apollo mailing list >>> [email protected] >>> http://mail.fruitfly.org/mailman/listinfo/apollo >>> >> >> _______________________________________________ >> apollo mailing list >> [email protected] >> http://mail.fruitfly.org/mailman/listinfo/apollo >> >> >
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