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
