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| Genes: |
A |
B |
A+B |
| Length: |
29 |
237 |
266 |
| Sequences: |
6 |
150 |
4 |
| Seq/Len: |
0.21 |
0.63 |
0.02 |
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Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
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HHblits results
Sequence A: (Date: 2015_06) BEFORE and AFTER the coverage filter was applied, to remove sequences that don't cover at least 75% of query length. Regions above red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len.
Sequence B: (Date: 2015_06) BEFORE and AFTER the coverage filter was applied, to remove sequences that don't cover at least 75% of query length. Regions above red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len.
[Show HHblits results] - Maybe useful in deciding what regions to trim. |
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| 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! |
| ID |
Seq/Len |
Name |
Options |
I_Prob |
Status |
| 5939 |
0.02 |
LpxT-PmrR |
Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06)
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Killed - Shared |
| 5899 |
0 |
PMRR_LPXT |
Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)
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Killed - Shared |
| 5898 |
0.02 |
PMRR_LPXT |
Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 4375 |
0 |
PMRR_LPXT |
Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06)
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Killed - Shared |