May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
Rpt3-Rpn5 Open
Genes: A B A+B
Length: 428 445 608
Sequences: 4205 1331 30
Seq/Len: 9.82 2.99 0.05
MirrorTree (Pazo et al. 2001) 0.86
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.07 0.00
2 0.03 0.07 0.01
5 0.03 0.08 0.01
10 0.04 0.09 0.02
20 0.04 0.10 0.03
100 0.06 0.11 0.12
∞ 0.13 0.15 0.37
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results
  • ERROR: Not enough sequences to run GREMLIN analysis on (0.05 < 0.6).
ID Seq/Len Name Options I_Prob Status
5798 0 Rpt3 Rpn5 Inparanoid 1 Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed
3348 0.53 Rpt3-Rpn5 Open Δgene:(0, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done
3341 0.05 Rpt3-Rpn5 Open Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) Killed - Shared
3338 0.01 Rpt3-Rpn5 Open Δgene:(1, 20) A:(1E-04, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
3333 0.04 Rpt3-Rpn5 Open Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) Killed - Shared
Page generated in 0.0476 seconds.