Mm9 multiple alignment

Mouse Mm9 multiple alignment/conservation track

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 self alignment	21	2654 Mb	0.0	10000	medium	14.458	N/A	2007-08-31
rat rn4	21	2718 Mb	0.160657	5000	medium	68.357	69.541	re-running 31 Aug
human hg18	24	3080 Mb	0.452619	3000	medium	38.499	35.201	2007-08-16
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	32.362	34.891	2007-09-05
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	1.933	6.495	2007-08-31

(*) 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, Y=15000, T=2 O=600, Q=mouse_rat.q E=55

query	abridged repeats	M	K	L	Q	Y
Rat rn4	yes	40M	4500	4500	mouse-rat	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	50	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 mouse-rat scoring matrix is:
A C G T A 91 -114 -31 -123 C -114 100 -125 -31 G -31 -125 100 -114 T -123 -31 -114 91 O=400 E=30		A C G T A 91 -90 -25 -100 C -90 100 -100 -25 G -25 -100 100 -90 T -100 -25 -90 91 O=400 E=30		A C G T A 56 -109 -45 -137 C -109 100 -103 -45 G -45 -103 100 -109 T -137 -45 -109 56 O=600 E=55

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);