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
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