PanTro3 conservation lastz parameters: Difference between revisions
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==See Also | ==See Also== | ||
<UL> | <UL> | ||
<LI>[[PanTro3 Genome size statistics]]</LI> | <LI>Chimp 12-way [[PanTro3 Genome size statistics]]</LI> | ||
<LI>[[PanTro3 conservation alignment]]</LI> | <LI>Chimp 12-way [[PanTro3 conservation alignment]]</LI> | ||
<LI>[[ | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
Latest revision as of 22:39, 18 May 2011
See Also
- Chimp 12-way PanTro3 Genome size statistics
- Chimp 12-way PanTro3 conservation alignment
- all other UCSC Multiple Alignments
| The default scoring matrix is: | The HoxD55 scoring matrix is: | The human-chimp.v2 scoring matrix is: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
O=400 E=30 |
O=400 E=30 |
O=600 E=150 |
do not edit, automatically generated table
| query | abridged repeats(no) |
M(0) | K(3000) | L(3000) | Q | Y(9400) | program run | E(30) | H(0) | O(400) | T(1) | chain table date |
% of panTro3 matched (chainLink table) |
% of query matched (chainLinkPanTro3) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Human hg19 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2011-02-23 | 95.597% | N/A |
| Orangutan ponAbe2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2011-03-06 | 89.586% | 87.748% |
| Rhesus rheMac2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2011-03-06 | 81.342% | 85.681% |
| Marmoset calJac3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2011-03-06 | 69.662% | 72.471% |
| Horse equCab2 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2011-03-06 | 56.504% | 65.863% |
| Dog canFam2 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2011-03-06 | 51.588% | 60.315% |
| Mouse mm9 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2011-03-07 | 32.044% | 35.182% |
| Rat rn4 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2011-03-17 | 30.350% | 34.038% |
| Opossum monDom5 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2011-03-11 | 13.743% | 11.337% |
| Chicken galGal3 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2011-03-02 | 4.557% | 11.116% |
| Zebrafish danRer7 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2011-03-01 | 2.558% | 5.821% |
