Mm9 multiple alignment
From genomewiki
Mouse Mm9 multiple alignment/conservation track
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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 The chrom count in the table below does not include haplotypes, chr*_random, chrUn or chrM unless chrUn or scaffolds are the only sequences for that assembly. The genome size has the same limitation as the chrom count, no randoms. Tree distances are from the hg18 28-way measurements, with ponAbe1 and calJac1 manually inserted into the tree. I believe we use "syntenic" nets on the organisms that are assembled into chromosomes. 1 Mb = 1000 * 1000 = 1,000,000 bases |
 30-way phylogenetic tree |
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 |
|---|---|---|---|---|---|---|---|---|
| mouse mm9 | 21 | 2654 Mb | 0.0 | |||||
| rat rn4 | 21 | 2718 Mb | 0.160657 | 3000 | medium | 68.357 | 69.541 | 16 August |
| human hg18 | 24 | 3080 Mb | 0.452619 | 3000 | medium | 38.499 | 35.201 | 16 August |
| Rhesus rheMac2 | 22 | 2864 Mb | 0.452745 | 3000 | medium | xx.123 | xx.456 | tbd |
| Orangutan ponAbe1 | 79553 | 3240 Mb | 0.453809 | 3000 | medium | xx.123 | xx.456 | tbd |
| Marmoset calJac1 | 49724 | 3029 Mb | 0.454272 | 3000 | medium | xx.123 | xx.456 | tbd |
| Chimp panTro2 | 25 | 3175 Mb | 0.454514 | 3000 | medium | xx.123 | xx.456 | tbd |
| GuineaPig cavPor2 | 295514 | 3403 Mb | 0.479871 | 3000 | medium | xx.123 | xx.456 | tbd |
| Horse equCab1 | 32 | 2056 Mb | 0.479871 | 3000 | medium | xx.123 | xx.456 | tbd |
| TreeShrew tupBel1 | 150851 | 3660 Mb | 0.494934 | 3000 | medium | xx.123 | xx.456 | tbd |
| Bushbaby otoGar1 | 120882 | 3420 Mb | 0.498957 | 3000 | medium | xx.123 | xx.456 | tbd |
| Armadillo dasNov1 | 304391 | 3856 Mb | 0.517360 | 3000 | medium | xx.123 | xx.456 | tbd |
| Rabbit oryCun1 | 215471 | 3464 Mb | 0.519779 | 3000 | medium | xx.123 | xx.456 | tbd |
| Cat felCat3 | 217790 | 4045 Mb | 0.530610 | 3000 | medium | xx.123 | xx.456 | tbd |
| Dog canFam2 | 39 | 2445 Mb | 0.533544 | 3000 | medium | xx.123 | xx.456 | tbd |
| Elephant loxAfr1 | 233134 | 3707 Mb | 0.536627 | 3000 | medium | xx.123 | xx.456 | tbd |
| Cow bosTau3 | 30 | 2434 Mb | 0.540852 | 3000 | medium | xx.123 | xx.456 | tbd |
| Hedgehog eriEur1 | 379801 | 3367 Mb | 0.632457 | 3000 | medium | xx.123 | xx.456 | tbd |
| Shrew sorAra1 | 262057 | 2936 Mb | 0.658734 | 3000 | medium | xx.123 | xx.456 | tbd |
| Tenrec echTel1 | 325491 | 3823 Mb | 0.666303 | 3000 | medium | xx.123 | xx.456 | tbd |
| Opossum monDom4 | 9 | 3431 Mb | 0.909852 | 5000 | loose | xx.123 | xx.456 | tbd |
| Platypus ornAna1 | 201522 | 1996 Mb | 1.165888 | 5000 | loose | xx.123 | xx.456 | tbd |
| Chicken galGal3 | 33 | 1032 Mb | 1.285399 | 5000 | loose | xx.123 | xx.456 | tbd |
| Lizard anoCar1 | 7233 | 1781 Mb | 1.404225 | 5000 | loose | xx.123 | xx.456 | tbd |
| X. tropicalis xenTro2 | 19759 | 1513 Mb | 1.726205 | 5000 | loose | xx.123 | xx.456 | tbd |
| Stickleback gasAcu1 | 21 | 400 Mb | 2.012649 | 5000 | loose | xx.123 | xx.456 | tbd |
| Zebrafish danRer4 | 25 | 1547 Mb | 2.027153 | 5000 | loose | xx.123 | xx.456 | tbd |
| Tetraodon tetNig1 | 21 | 217 Mb | 2.051015 | 5000 | loose | xx.123 | xx.456 | tbd |
| Fugu fr2 | 1 | 400 Mb | 2.086669 | 5000 | loose | xx.123 | xx.456 | tbd |
| Medaka oryLat1 | 24 | 724 Mb | 2.200402 | 5000 | loose | xx.123 | xx.456 | tbd |
(*) chrom count does not include haplotypes, chr*_random, chrUn or chrM unless chrUn or scaffolds are the only sequences for that assembly.
The genome size has the same limitation as the chrom count, no randoms.
Tree distances are from the hg18 28-way measurements, with ponAbe1 and calJac1 manually inserted into the tree.
blastz alignment parameters details
One special run, Rat rn4, M=40M, K=4500, L=4500, Q=default, Y=15000, T=2 O=600, H=2000, Q=human_chimp.v2.q E=150
| query | abridged repeats |
M | K | L | Q | Y |
|---|---|---|---|---|---|---|
| Rat rn4 | yes | 40M | 4500 | 4500 | default | 15000 |
| Human hg18 | yes | 40M | 3K | 3K | default | 9400 |
| Rhesus rheMac2 | no | 40M | 3K | 3K | default | 9400 |
| Orangutan ponAbe1 | no | 50 | 3K | 3K | default | 9400 |
| Marmoset calJac1 | no | 50 | 3K | 3K | default | 9400 |
| Chimp panTro2 | yes | 40M | 3K | 3K | default | 9400 |
| GuineaPig cavPor2 | no | 50 | 3K | 3K | default | 9400 |
| Horse equCab1 | no | 40M | 3K | 3K | default | 9400 |
| TreeShrew tupBel1 | no | 50 | 3K | 3K | default | 9400 |
| Bushbaby otoGar1 | no | 50 | 3K | 3K | default | 9400 |
| Armadillo dasNov1 | no | 50 | 3K | 3K | default | 9400 |
| Rabbit oryCun1 | no | 50 | 3K | 3K | default | 9400 |
| Cat felCat3 | no | 50 | 3K | 3K | default | 9400 |
| Dog canFam2 | yes | 40M | 3K | 3K | default | 9400 |
| Elephant loxAfr1 | no | 50 | 3K | 3K | default | 9400 |
| Cow bosTau3 | no | 40M | 3K | 3K | default | 9400 |
| Hedgehog eriEur1 | no | 50 | 3K | 3K | default | 9400 |
| Shrew sorAra1 | no | 50 | 3K | 3K | default | 9400 |
| Tenrec echTel1 | no | 50 | 3K | 3K | default | 9400 |
| Opossum monDom4 | no | 50 | 2200 | 6000 | HoxD55 | 3400 |
| Platypus ornAna1 | no | 50 | 2200 | 6000 | HoxD55 | 3400 |
| Chicken galGal3 | yes | 40M | 2200 | 6000 | HoxD55 | 3400 |
| Lizard anoCar1 | no | 50 | 2200 | 6000 | HoxD55 | 3400 |
| X_tropicalis xenTro2 | no | 50 | 2200 | 6000 | HoxD55 | 3400 |
| Stickleback gasAcu1 | no | 40M | 2200 | 6000 | HoxD55 | 3400 |
| Zebrafish danRer4 | yes | 40M | 2200 | 6000 | HoxD55 | 3400 |
| Tetraodon tetNig1 | no | 40M | 2200 | 6000 | HoxD55 | 3400 |
| Fugu fr2 | no | 40M | 2200 | 6000 | HoxD55 | 3400 |
| Medaka oryLat1 | no | 40M | 2200 | 6000 | HoxD55 | 3400 |
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.
| The default scoring matrix is: | The HoxD55 scoring matrix is: | The human-chimp scoring matrix is: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
O=400 E=30 |
O=400 E=30 |
O=600 E=150 |
axtChain 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
the tree diagram
((((((((
(((Mouse_mm9:0.076274,Rat_rn4:0.084383):0.200607,
GuineaPig_cavPor2:0.202990):0.034350,
Rabbit_oryCun1:0.208548):0.014587,
((((((Human_hg18:0.005873,Chimp_panTro2:0.007668):0.013037,
Orangutan_ponAbe1:0.02):0.013037,Rhesus_rheMac2:0.031973):0.0365,
Marmoset_calJac1:0.07):0.0365,Bushbaby_otoGar1:0.151185):0.015682,
TreeShrew_tupBel1:0.162844):0.006272):0.019763,
((Shrew_sorAra1:0.248532,Hedgehog_eriEur1:0.222255):0.045693,
(((Dog_canFam2:0.101137,Cat_felCat3:0.098203):0.048213,
Horse_equCab1:0.099323):0.007287,
Cow_bosTau3:0.163945):0.012398):0.018928):0.030081,
(Armadillo_dasNov1:0.133274,(Elephant_loxAfr1:0.103030,
Tenrec_echTel1:0.232706):0.049511):0.008424):0.213469,
Opossum_monDom4:0.320721):0.088647,
Platypus_ornAna1:0.488110):0.118797,
(Chicken_galGal3:0.395136,Lizard_anoCar1:0.513962):0.093688):0.151358,
Frog_xenTro2:0.778272):0.174596,
(((Tetraodon_tetNig1:0.203933,Fugu_fr2:0.239587):0.203949,
(Stickleback_gasAcu1:0.314162,Medaka_oryLat1:0.501915):0.055354):0.346008,
Zebrafish_danRer4:0.730028):0.174596);
