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Genes: |
A |
B |
A+B |
Length: |
101 |
50 |
145 |
Sequences: |
7718 |
851 |
49 |
Seq/Len: |
76.42 |
17.02 |
0.34 |
MirrorTree (Pazo et al. 2001) |
0.68 |
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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 |
9986 |
2.03 |
beta flap (A, 50-660) (A, 100-200) |
Δgene:(1, 100) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06)
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0.13 |
Done - Shared |
9985 |
0.34 |
beta flap (A, 50-660) (A, 100-200) |
Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06)
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Killed - Shared |
9984 |
0.01 |
beta flap (A, 50-660) (A, 100-200) |
Δgene:(1, 20) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06)
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Killed - Shared |
9983 |
0.15 |
beta flap (A, 50-660) (A, 100-200) |
Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)
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Killed - Shared |