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Yummy_BmdBA2Domain_BmdC

Genes: A B A+B
Length: 325 481 794
Sequences: 174 36712 41
Seq/Len: 0.54 76.32 0.05
MirrorTree (Pazo et al. 2001) 0.39
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.

Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.08 0.02
2 0.01 0.11 0.02
5 0.01 0.14 0.03
10 0.01 0.17 0.04
20 0.01 0.19 0.05
100 0.01 0.24 0.09
0.03 0.30 0.15
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
7326 0.04 BmdB_BmdC_alignment_EvalueLowered Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (r132) Killed
7325 0.01 BmdB_BmdC_alignment_EvalueLowered Δgene:(1, 1) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed
7324 0.18 YUMMY_BmdB_BmdC_Take2 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7323 0.05 Yummy_BmdBA2Domain_BmdC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared

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