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PcrA_CT_conserved vs RNAP beta 1st half

Genes: A B A+B
Length: 49 600 649
Sequences: 10 1433 1
Seq/Len: 0.2 2.39 0
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 0.56 0.09 0.00
2 0.56 0.09 0.00
5 0.56 0.09 0.00
10 0.56 0.09 0.00
20 0.56 0.09 0.00
100 0.56 0.09 0.00
0.56 0.09 0.00
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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 < 0.6).
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.56 > 0.4) of paralogs.

ID Seq/Len Name Options I_Prob Status
8206 0.11 PcrA_CT_conserved vs RNAP beta 1st half Δgene:(1, ∞) A:(1E-04, 2) B:(1E-10, 2) msa: HHblits (2015_06) 0.00 Done - Shared
8205 0.11 PcrA_CT_conserved vs RNAP beta 1st half Δgene:(1, ∞) A:(1E-04, 2) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8204 0 PcrA_CT_conserved vs RNAP beta 1st half Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared

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