Mm9 multiple alignment: Difference between revisions
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<TABLE BORDER=1> | <TABLE BORDER=1> | ||
<TR> | <TR> | ||
<TH> | <TH>name db</TH> | ||
<TH>chrom<BR>count</TH> | |||
<TH>genome<BR>size</TH> | |||
<TH>tree<BR>distance</TH> | <TH>tree<BR>distance</TH> | ||
<TH>axtChain<BR>minScore</TH> | <TH>axtChain<BR>minScore</TH> | ||
<TH>axtChain<BR>linearGap</TH> | <TH>axtChain<BR>linearGap</TH> | ||
| Line 17: | Line 18: | ||
<TR> | <TR> | ||
<TH>rat rn4</TH> | <TH>rat rn4</TH> | ||
<TD> | <TD>21</TD> | ||
<TD>2,702 Mb</TD> | <TD>2,702 Mb</TD> | ||
<TD>0.1587</TD> | |||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
| Line 28: | Line 30: | ||
<TR> | <TR> | ||
<TH>human hg18</TH> | <TH>human hg18</TH> | ||
<TD> | <TD>24</TD> | ||
<TD>2,963 Mb</TD> | <TD>2,963 Mb</TD> | ||
<TD>0.4667</TD> | |||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
| Line 38: | Line 41: | ||
<TR> | <TR> | ||
< | <TD>Chimp panTro2</TD> | ||
<TD>25</TD> | |||
<TD>3028 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>tbd ponAbe1</TD> | ||
<TD>79553</TD> | |||
<TD>3090 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Rhesus rheMac2</TD> | ||
<TD>22</TD> | |||
<TD>2731 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Bushbaby otoGar1</TD> | ||
<TD>120882</TD> | |||
<TD>3261 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>tbd calJac1</TD> | ||
<TD>49724</TD> | |||
<TD>2889 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>TreeShrew tupBel1</TD> | ||
<TD>150851</TD> | |||
<TD>3491 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>GuineaPig cavPor2</TD> | ||
<TD>295514</TD> | |||
<TD>3246 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Rabbit oryCun1</TD> | ||
<TD>215471</TD> | |||
<TD>3303 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Shrew sorAra1</TD> | ||
<TD>262057</TD> | |||
<TD>2800 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Hedgehog eriEur1</TD> | ||
<TD>379801</TD> | |||
<TD>3211 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Dog canFam2</TD> | ||
<TD>39</TD> | |||
<TD>2331 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Cat felCat3</TD> | ||
<TD>217790</TD> | |||
<TD>3858 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Horse equCab1</TD> | ||
<TD>32</TD> | |||
<TD>1961 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Cow bosTau3</TD> | ||
<TD>30</TD> | |||
<TD>2321 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Armadillo dasNov1</TD> | ||
<TD>304391</TD> | |||
<TD>3678 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Elephant loxAfr1</TD> | ||
<TD>233134</TD> | |||
<TD>3535 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Tenrec echTel1</TD> | ||
<TD>325491</TD> | |||
<TD>3646 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Opossum monDom4</TD> | ||
<TD>9</TD> | |||
<TD>3272 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Platypus ornAna1</TD> | ||
<TD>201522</TD> | |||
<TD>1904 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Chicken galGal3</TD> | ||
<TD>33</TD> | |||
<TD>984 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Lizard anoCar1</TD> | ||
<TD>7233</TD> | |||
<TD>1699 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>X. tropicalis xenTro2</TD> | ||
<TD>19759</TD> | |||
<TD>1443 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Tetraodon tetNig1</TD> | ||
<TD>21</TD> | |||
<TD>207 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Fugu fr2</TD> | ||
<TD>1</TD> | |||
<TD>381 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Stickleback gasAcu1</TD> | ||
<TD>21</TD> | |||
<TD>382 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Medaka oryLat1</TD> | ||
<TD>24</TD> | |||
<TD>690 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
<TR> | <TR> | ||
< | <TD>Zebrafish danRer4</TD> | ||
<TD>25</TD> | |||
<TD>1475 Mb</TD> | |||
<TD>X.xxxx</TD> | <TD>X.xxxx</TD> | ||
<TD>3000</TD> | <TD>3000</TD> | ||
<TD>medium</TD> | <TD>medium</TD> | ||
<TD>xx.123</TD> | <TD>xx.123</TD> | ||
<TD>xx.456</TD> | <TD>xx.456</TD> | ||
<TD> | <TD>tbd</TD> | ||
<TR> | </TR> | ||
</TABLE> | </TABLE> | ||
Revision as of 23:33, 17 August 2007
To avoid artifacts in downstream processing of the UCSC multiple alignments, it is important to be careful on the use of the parameters used in the blastz processing pipeline. There are a number of steps in the pipeline and a variety of tunable parameters involved. This page will track the various parameters used in the alignments as they proceed toward the completion of a multiple alignment conservation track on the mm9 mouse (NCBI build 37) assembly
axtChain parameters and end results
| name db | chrom count |
genome size |
tree distance |
axtChain minScore |
axtChain linearGap |
% of mm9 matched |
% of other matched by mm9 |
done |
|---|---|---|---|---|---|---|---|---|
| rat rn4 | 21 | 2,702 Mb | 0.1587 | 3000 | medium | 68.357 | 69.541 | 16 August |
| human hg18 | 24 | 2,963 Mb | 0.4667 | 3000 | medium | 38.499 | 35.201 | 16 August |
| Chimp panTro2 | 25 | 3028 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| tbd ponAbe1 | 79553 | 3090 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Rhesus rheMac2 | 22 | 2731 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Bushbaby otoGar1 | 120882 | 3261 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| tbd calJac1 | 49724 | 2889 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| TreeShrew tupBel1 | 150851 | 3491 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| GuineaPig cavPor2 | 295514 | 3246 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Rabbit oryCun1 | 215471 | 3303 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Shrew sorAra1 | 262057 | 2800 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Hedgehog eriEur1 | 379801 | 3211 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Dog canFam2 | 39 | 2331 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Cat felCat3 | 217790 | 3858 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Horse equCab1 | 32 | 1961 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Cow bosTau3 | 30 | 2321 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Armadillo dasNov1 | 304391 | 3678 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Elephant loxAfr1 | 233134 | 3535 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Tenrec echTel1 | 325491 | 3646 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Opossum monDom4 | 9 | 3272 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Platypus ornAna1 | 201522 | 1904 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Chicken galGal3 | 33 | 984 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Lizard anoCar1 | 7233 | 1699 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| X. tropicalis xenTro2 | 19759 | 1443 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Tetraodon tetNig1 | 21 | 207 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Fugu fr2 | 1 | 381 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Stickleback gasAcu1 | 21 | 382 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Medaka oryLat1 | 24 | 690 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
| Zebrafish danRer4 | 25 | 1475 Mb | X.xxxx | 3000 | medium | xx.123 | xx.456 | tbd |
blastz alignment parameters details
| target | query | abridged repeats |
target size (overlap) |
query size (overlap) |
H | M |
|---|---|---|---|---|---|---|
| mm9 | rat rn4 | yes B=0 |
10M (10K) | 10M (0) | 2000 | 40M |
| human hg18 | mm9 | yes B=0 |
10M (0) | 10M (10K) | 2000 | 40M |
default blastz parameters
m=80 v=0 B=2 C=0 E=30 G=0 H=0 K=3000 L=K
M=0 O=400 P=1 R=0 T=1 W=8 X=10*(A-to-A match score)
Y=O+300*E Z=1
From the blastz usage message:
Default values are given in parentheses.
m(80M) bytes of space for trace-back information
v(0) 0: quiet; 1: verbose progress reports to stderr
B(2) 0: single strand; >0: both strands
C(0) 0: no chaining; 1: just output chain; 2: chain and extend;
3: just output HSPs
E(30) gap-extension penalty.
G(0) diagonal chaining penalty.
H(0) interpolate between alignments at threshold K = argument.
K(3000) threshold for MSPs
L(K) threshold for gapped alignments
M(0) mask any base in seq1 hit this many times; 0 = no dynamic masking
O(400) gap-open penalty.
P(1) 0: entropy not used; 1: entropy used; >1 entropy with feedback.
Q load the scoring matrix from a file.
R(0) antidiagonal chaining penalty.
T(1) 0: W-bp words; 1: 12of19; 2: 12of19 without transitions.
3: 14of22; 4: 14of22 without transitions.
W(8) word size (unused unless T=0)
X(10*(A-to-A match score)) X-drop parameter for ungapped extension.
Y(O+300E) X-drop parameter for gapped extension.
Z(1) increment between successive words in sequence 1.
matrix parameters
The "medium" gap score matrix, tuned for the mouse-human distance is:
tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300
The "loose" gap score matrix, tuned for the chicken-human distance is:
tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
