Does anyone know the genome alignment format like this?

Question

[wang.yiguan]

I have the whole genome alignment results from two species, but I am confused about the results format. Does anyone know the format, and can you make an explanation? Thank you very much!

##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
##gapPenalties=axtChain O=400 E=30
# lastz.v1.04.00 --masking=50 --hspthresh=2200 --ydrop=3400 --gappedthresh=4000 --inner=2000 --format=axt --output=xxxxxx.axt
#
# hsp_threshold      = 2200
# gapped_threshold   = 4000
# x_drop             = 910
# y_drop             = 3400
# gap_open_penalty   = 400
# gap_extend_penalty = 30
#        A    C    G    T
#   A   91 -114  -31 -123
#   C -114  100 -125  -31
#   G  -31 -125  100 -114
#   T -123  -31 -114   91
chain 589271 MTTC0100016x.1 36216 + 2 13582 scf718000060xxxx 211718 + 199665 211441 1250
16      4       0
59      0       8
5       0       12
9       0       11
54      19      0
9       140     118
34      1       0
29      2       0
8       20      0
69      0       7
133     9       0
42      2       0
25      10      0
88      1       0
78      6       0
39      0       6
36      0       5
55      1       0
20      8       0
28      0       1
37      66      0
68      8       0
38      0       2
21      1       0
73      1       0
61      0       21
77      0       1
13      0       22
26      1       0
44      0       1

Answer 1

[h.mon]

Your post would be a good candidate for the google your own title™, had you used a more informative title. This is an axt alignment file.

But wait! No, this is an axtChain file:

The axtNet and axtChain alignments are produced by processing the alignment files with additional utilities written by Jim Kent at UCSC.

Probably used to transfer coordinates between genome versions.

P. S.: how you obtained the file? Did you ran the alignment yourself or downloaded the file? Which software you used to align the genomes? And so on... All this information is useful for answering questions, but alas, you didn't provide any of it.

[wang.yiguan]

Thanks for providing me these info. I found some documents about the format: https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/m5eTOXbkiec http://genome.ucsc.edu/goldenPath/help/chain.html