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OPENSEQ.org
ACRA_TOLC
Genes: A B A+B
Length: 397 493 822
Sequences: 3744 1770 25
Seq/Len: 9.43 3.59 0.03
MirrorTree (Pazo et al. 2001) 0.95
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 0.01 0.03
2 0.02 0.01 0.04
5 0.03 0.02 0.05
10 0.05 0.02 0.07
20 0.06 0.03 0.10
100 0.08 0.05 0.23
∞ 0.16 0.11 0.90
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 (0.03 < 0.6).
ID Seq/Len Name Options I_Prob Status
5917 6.61 acra-tolc Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.99 Done - Shared
4292 2.61 ACRA_TOLC Δgene:(1, 5) A:(1E-80, 4) B:(1E-40, 4) msa: Jackhmmer (2015_06) 1.00 Done
4290 0.35 ACRA_TOLC Δgene:(1, 1) A:(1E-80, 4) B:(1E-40, 4) msa: Jackhmmer (2015_06) 0.01 Done
4288 0.03 ACRA_TOLC Δgene:(1, 1) A:(1E-80, 4) B:(1E-60, 4) msa: Jackhmmer (2015_06) Killed
4286 0.02 ACRA_TOLC Δgene:(1, 1) A:(1E-80, 4) B:(1E-80, 4) msa: Jackhmmer (2015_06) Killed
4283 4.75 ACRA_TOLC Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.99 Done
4276 9.31 ACRA_TOLC Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 1.00 Done
0669 4.67 A-C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.99 Done
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