|
| Genes: |
A |
B |
A+B |
| Length: |
437 |
102 |
539 |
| Sequences: |
2108 |
1 |
1 |
| Seq/Len: |
4.82 |
0.01 |
0 |
|
|
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 |
| 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 |