Mm9 multiple alignment

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	2702 Mb	0.160657	3000	medium	68.357	69.541	16 August
human hg18	24	2963 Mb	0.452619	3000	medium	38.499	35.201	16 August
Rhesus rheMac2	22	2731 Mb	0.452745	3000	medium	xx.123	xx.456	tbd
Orangutan ponAbe1	79553	3090 Mb	0.453809	3000	medium	xx.123	xx.456	tbd
Marmoset calJac1	49724	2889 Mb	0.454272	3000	medium	xx.123	xx.456	tbd
Chimp panTro2	25	3028 Mb	0.454514	3000	medium	xx.123	xx.456	tbd
GuineaPig cavPor2	295514	3246 Mb	0.479871	3000	medium	xx.123	xx.456	tbd
Horse equCab1	32	1961 Mb	0.479871	3000	medium	xx.123	xx.456	tbd
TreeShrew tupBel1	150851	3491 Mb	0.494934	3000	medium	xx.123	xx.456	tbd
Bushbaby otoGar1	120882	3261 Mb	0.498957	3000	medium	xx.123	xx.456	tbd
Armadillo dasNov1	304391	3678 Mb	0.517360	3000	medium	xx.123	xx.456	tbd
Rabbit oryCun1	215471	3303 Mb	0.519779	3000	medium	xx.123	xx.456	tbd
Cat felCat3	217790	3858 Mb	0.530610	3000	medium	xx.123	xx.456	tbd
Dog canFam2	39	2331 Mb	0.533544	3000	medium	xx.123	xx.456	tbd
Elephant loxAfr1	233134	3535 Mb	0.536627	3000	medium	xx.123	xx.456	tbd
Cow bosTau3	30	2321 Mb	0.540852	3000	medium	xx.123	xx.456	tbd
Hedgehog eriEur1	379801	3211 Mb	0.632457	3000	medium	xx.123	xx.456	tbd
Shrew sorAra1	262057	2800 Mb	0.658734	3000	medium	xx.123	xx.456	tbd
Tenrec echTel1	325491	3646 Mb	0.666303	3000	medium	xx.123	xx.456	tbd
Opossum monDom4	9	3272 Mb	0.909852	5000	loose	xx.123	xx.456	tbd
Platypus ornAna1	201522	1904 Mb	1.165888	5000	loose	xx.123	xx.456	tbd
Chicken galGal3	33	984 Mb	1.285399	5000	loose	xx.123	xx.456	tbd
Lizard anoCar1	7233	1699 Mb	1.404225x	5000	loose	xx.123	xx.456	tbd
X. tropicalis xenTro2	19759	1443 Mb	1.726205	5000	loose	xx.123	xx.456	tbd
Stickleback gasAcu1	21	382 Mb	2.012649	5000	loose	xx.123	xx.456	tbd
Zebrafish danRer4	25	1475 Mb	2.027153	5000	loose	xx.123	xx.456	tbd
Tetraodon tetNig1	21	207 Mb	2.051015	5000	loose	xx.123	xx.456	tbd
Fugu fr2	1	381 Mb	2.086669	5000	loose	xx.123	xx.456	tbd
Medaka oryLat1	24	690 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.

chrom 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

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