May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
Sec Y - PpiD (E coli)
Genes: A B A+B
Length: 437 102 517
Sequences: 2583 4894 12
Seq/Len: 5.91 47.98 0.02
MirrorTree (Pazo et al. 2001) 0.57
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 0.04 0.00
2 0.01 0.06 0.00
5 0.01 0.06 0.00
10 0.01 0.08 0.01
20 0.01 0.08 0.02
100 0.02 0.11 0.31
∞ 0.03 0.19 1.72
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 (0.02 < 0.6).
ID Seq/Len Name Options I_Prob Status
13316 2.24 Sec Y - PpiD (E coli) 30 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13281 2.16 Sec Y - PpiD (E coli) 20 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.02 Done - Shared
13273 0 Sec Y - PpiD (E coli) 20 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed - Shared
13272 0 Sec Y - PpiD (E coli) 20 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed - Shared
13270 0 Sec Y - PpiD (E coli) 20 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed - Shared
13265 0.02 Sec Y - PpiD (E coli) Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.0131 seconds.