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Genes: |
A |
B |
A+B |
Length: |
513 |
460 |
961 |
Sequences: |
1366 |
1091 |
846 |
Seq/Len: |
2.66 |
2.37 |
0.88 |
MirrorTree (Pazo et al. 2001) |
0.93 |
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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: 2013_03) 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: 2013_03) 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 |
0192 |
1.22 |
ATPA - ATPB decreasing evalue to 1E-401E-60 |
Δgene:(1, 20) A:(1E-80, 4) B:(1E-80, 4) msa: Jackhmmer (2014_03)
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1.00 |
Done |
0191 |
0 |
ATPA - ATPB decreasing evalue to 1E-401E-60 |
Δgene:(1, 20) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2014_03)
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|
Killed |
0190 |
0 |
ATPA - ATPB decreasing evalue to 1E-401E-60 |
Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03)
|
|
Killed |
0020 |
0.01 |
ATPA - ATPB decreasing evalue to 1E-401E-60 |
Δgene:(1, 20) A:(1E-40, 8) B:(1E-60, 8) (2013_03)
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Killed - Shared |
0019 |
0.9 |
ATPA - ATPB decreasing evalue to 1E-60 |
Δgene:(1, 20) A:(1E-60, 8) B:(1E-60, 8) (2013_03)
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1.00 |
Done - Shared |
0018 |
0.88 |
ATPA - ATPB decreasing evalue |
Δgene:(1, 20) A:(1E-80, 8) B:(1E-80, 8) (2013_03)
|
1.00 |
Done - Shared |
0017 |
0 |
ATPA - ATPB |
Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03)
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Killed - Shared |