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update with KH (c.intestinalis)
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Hyungro Lee committed Jul 6, 2015
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45 changes: 42 additions & 3 deletions docs/source/results.rst
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Expand Up @@ -87,9 +87,48 @@ Extra Files
* :download:`CR1.en.pep <sample/dm3/data/info/full/CR1/CR1.en.pep.txt>`
* :download:`nonltr.gff3 <sample/dm3/data/info/nonltr.gff3.txt>`

d. pulex MGEScan1.3.1 No MPI 4 hrs 5mins 14,697 secs 1hr 8mins 4,127 secs 2 hrs 57 mins 10,570 secs
MGEScan2 No MPI 2 hrs 36 mins 9,414 secs 46 mins 2,780 secs 2 hrs 36 mins 9,414 secs
MGEScan2 MPI (4 Proc) 1hr 3mins 3,823 secs 4 mins 222 secs 1 hr 3mins 3,823 secs
C. intestinalis
-------------------------------------------------------------------------------

* :download:`KH.gff3 <sample/KH.gff3.txt>`
* :download:`KH.ltr.out <sample/KH.ltr.out.txt>`
* :download:`KH.en <sample/KH.en.txt>`
* :download:`KH.rt <sample/KH.rt.txt>`


Evaluation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. list-table:: Elapsed time for MGEScan (KH)
:header-rows: 1

* - Program
- Total
- nonLTR
- LTR
- Options
* - MGEScan1.3.1
- 4 hrs 5mins (14,697 secs)
- 1hr 8mins (4,127 secs)
- 2 hrs 57 mins (10,570 secs)
- HMMER 2.3.2, no MPI
* - MGEScan2
- 2 hrs 36 mins (9,414 secs)
- 46 mins (2,780 secs)
- 2 hrs 36 mins (9,414 secs)
- HMMER 3.1b1, no MPI
* - MGEScan2 with MPI
- 1hr 3mins (3,823 secs)
- 4 mins (222 secs)
- 1 hr 3mins (3,823 secs)
- HMMER 3.1b1, MPI with 4 processors

Extra Files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

* :download:`KH.tar.gz <sample/KH.tar.gz>`


c. intestinalis exp1 MGEScan1.3.1 No MPI 3 hrs 34 mins 12,837 secs 21 mins 1,256 secs 3hrs 13 mins 11,581 secs
MGEScan2 No MPI 2 hrs 23 mins 8,604 secs 　 42 secs 2 hrs 23 mins 8,604 secs
MGEScan2 MPI (4 Proc) 50 mins 2,949 secs 　 13 secs 50 mins 2,949 secs
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4 changes: 4 additions & 0 deletions docs/source/sample/KH.en.txt
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tmp-------------------------------------
L1_HT000162.1.fa_134792_2 - 1000 1.0e+00
tmp-------------------------------------
RTE_HT000798.1.fa_3113_1 RTE 5.7e-62 3.2e-39
39 changes: 39 additions & 0 deletions docs/source/sample/KH.gff3.txt
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track name=LTR description="MGEScan-LTR" color=0,0,255,
chr1 MGEScan_LTR mobile_genetic_element 925586 938210 . + . ID=1_1.fa_1;name=cluster_1
chr12 MGEScan_LTR mobile_genetic_element 5263373 5272260 . - . ID=1_12.fa_1;name=cluster_1
chr1 MGEScan_LTR mobile_genetic_element 4641060 4659435 . + . ID=2_1.fa_2;name=cluster_2
chr10 MGEScan_LTR mobile_genetic_element 1052058 1057579 . + . ID=3_10.fa_1;name=cluster_3
chr14 MGEScan_LTR mobile_genetic_element 11206 25355 . - . ID=4_14.fa_1;name=cluster_4
chr2 MGEScan_LTR mobile_genetic_element 404649 415823 . - . ID=5_2.fa_1;name=cluster_5
HT000034.1 MGEScan_LTR mobile_genetic_element 135507 146902 . + . ID=5_HT000034.1.fa_1;name=cluster_5
HT000016.1 MGEScan_LTR mobile_genetic_element 144326 152574 . + . ID=5_HT000016.1.fa_1;name=cluster_5
HT001072.1 MGEScan_LTR mobile_genetic_element 14153 26032 . - . ID=5_HT001072.1.fa_1;name=cluster_5
chr3 MGEScan_LTR mobile_genetic_element 5392337 5396563 . - . ID=6_3.fa_1;name=cluster_6
chr6 MGEScan_LTR mobile_genetic_element 1545424 1556391 . - . ID=7_6.fa_1;name=cluster_7
HT000033.1 MGEScan_LTR mobile_genetic_element 11363 25877 . - . ID=8_HT000033.1.fa_1;name=cluster_8
HT000034.1 MGEScan_LTR mobile_genetic_element 238234 253080 . + . ID=9_HT000034.1.fa_2;name=cluster_9
HT000062.1 MGEScan_LTR mobile_genetic_element 31016 43034 . + . ID=10_HT000062.1.fa_1;name=cluster_10
HT000103.1 MGEScan_LTR mobile_genetic_element 1163 20052 . - . ID=11_HT000103.1.fa_1;name=cluster_11
HT001083.1 MGEScan_LTR mobile_genetic_element 32737 50836 . - . ID=11_HT001083.1.fa_1;name=cluster_11
HT000117.1 MGEScan_LTR mobile_genetic_element 16128 18771 . + . ID=12_HT000117.1.fa_1;name=cluster_12
HT000117.1 MGEScan_LTR mobile_genetic_element 18817 21780 . - . ID=13_HT000117.1.fa_2;name=cluster_13
HT000122.1 MGEScan_LTR mobile_genetic_element 230019 238462 . + . ID=14_HT000122.1.fa_1;name=cluster_14
HT000122.1 MGEScan_LTR mobile_genetic_element 238551 245059 . - . ID=15_HT000122.1.fa_2;name=cluster_15
HT000179.1 MGEScan_LTR mobile_genetic_element 28984 34916 . + . ID=16_HT000179.1.fa_1;name=cluster_16
HT000302.1 MGEScan_LTR mobile_genetic_element 579 4136 . - . ID=17_HT000302.1.fa_1;name=cluster_17
HT000315.1 MGEScan_LTR mobile_genetic_element 7970 12476 . - . ID=18_HT000315.1.fa_1;name=cluster_18
HT000320.1 MGEScan_LTR mobile_genetic_element 839 7294 . - . ID=19_HT000320.1.fa_1;name=cluster_19
HT000417.1 MGEScan_LTR mobile_genetic_element 1371 8648 . + . ID=20_HT000417.1.fa_1;name=cluster_20
HT000442.1 MGEScan_LTR mobile_genetic_element 1947 6653 . + . ID=21_HT000442.1.fa_1;name=cluster_21
HT000461.1 MGEScan_LTR mobile_genetic_element 3339 6894 . - . ID=22_HT000461.1.fa_1;name=cluster_22
HT001087.1 MGEScan_LTR mobile_genetic_element 40580 51573 . + . ID=23_HT001087.1.fa_1;name=cluster_23
HT001108.1 MGEScan_LTR mobile_genetic_element 27414 40703 . + . ID=24_HT001108.1.fa_1;name=cluster_24
HT001164.1 MGEScan_LTR mobile_genetic_element 7608 12902 . + . ID=25_HT001164.1.fa_1;name=cluster_25
HT001193.1 MGEScan_LTR mobile_genetic_element 14835 20424 . - . ID=26_HT001193.1.fa_1;name=cluster_26
HT001216.1 MGEScan_LTR mobile_genetic_element 9475 14943 . + . ID=27_HT001216.1.fa_1;name=cluster_27
HT001239.1 MGEScan_LTR mobile_genetic_element 13378 18377 . - . ID=28_HT001239.1.fa_1;name=cluster_28
track name=nonLTR description="MGEScan-nonLTR" color=255,0,0
HT000162.1 MGEScan_nonLTR mobile_genetic_element 134792 140657 . . . ID=HT000162.1.fa_134792
HT000798.1 MGEScan_nonLTR mobile_genetic_element 3113 6382 . . . ID=HT000798.1.fa_3113
HT001007.1 MGEScan_nonLTR mobile_genetic_element 359 3504 . . . ID=HT001007.1.fa_359
HT000922.1 MGEScan_nonLTR mobile_genetic_element 1142 4511 . . . ID=HT000922.1.fa_1142
62 changes: 62 additions & 0 deletions docs/source/sample/KH.ltr.out.txt
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1----------
1.fa_1 925586 925781 938010 938210 + 196 201 12625 2.1e-16 - - - - - -
12.fa_1 5263373 5263549 5272086 5272260 - 177 175 8888 2.6e-16 - - - - - -
2----------***
1.fa_2 4641060 4641223 4659272 4659435 + 164 164 18376 2e-15 TTGG TTGT TG CA TG CA
3----------***
10.fa_1 1052058 1052238 1057399 1057579 + 181 181 5522 6.72e-106 TTAC TTAC TGT ACA TGT ACA
4----------
14.fa_1 11206 12169 24410 25355 - 964 946 14150 6.1e-21 - - - - - -
5----------
2.fa_1 404649 404849 415626 415823 - 201 198 11175 8.525e-102 - - - - - -
HT000034.1.fa_1 135507 135697 146712 146902 + 191 191 11396 2.8e-29 GTTT GTCT TG CA TG CA
HT000016.1.fa_1 144326 144552 152377 152574 + 227 198 8249 1.1e-23 ACAA AAAA TG CA TG CA
HT001072.1.fa_1 14153 14354 25836 26032 - 202 197 11880 9.1e-22 - - - - - -
6----------***
3.fa_1 5392337 5392586 5396314 5396563 - 250 250 4227 5.2e-79 CCTAA CCTAA TGT ACA TGT ACA
7----------
6.fa_1 1545424 1545684 1556117 1556391 - 261 275 10968 2.42e-90 - - - - - -
8----------
HT000033.1.fa_1 11363 11652 25580 25877 - 290 298 14515 2.9e-23 - - - - - -
9----------
HT000034.1.fa_2 238234 238562 252772 253080 + 329 309 14847 1.008e-53 - - - - - -
10----------
HT000062.1.fa_1 31016 31149 42902 43034 + 134 133 12019 1.428e-46 - - - - - -
11----------
HT000103.1.fa_1 1163 1341 19884 20052 - 179 169 18890 6e-18 - - - - - -
HT001083.1.fa_1 32737 32972 50607 50836 - 236 230 18100 2.4e-23 - - - - - -
12----------
HT000117.1.fa_1 16128 16338 18561 18771 + 211 211 2644 1.475e-20 - - - - - -
13----------
HT000117.1.fa_2 18817 18970 21631 21780 - 154 150 2964 8.8e-26 AAAA AAAA TGT CA TGT CA
14----------
HT000122.1.fa_1 230019 230595 237885 238462 + 577 578 8444 2.673e-87 - - - - - -
15----------
HT000122.1.fa_2 238551 238791 244813 245059 - 241 247 6509 6.5e-12 TGTTA TGGTA TGT ACA TGT ACA
16----------
HT000179.1.fa_1 28984 29439 34461 34916 + 456 456 5933 1.424e-48 - - - - - -
17----------
HT000302.1.fa_1 579 949 3755 4136 - 371 382 3558 1.5e-16 - - - - - -
18----------
HT000315.1.fa_1 7970 8158 12287 12476 - 189 190 4507 4.836e-61 - - - - - -
19----------***
HT000320.1.fa_1 839 1306 6826 7294 - 468 469 6456 6.05e-84 GAGT GACT TGT CA TGT ACA
20----------
HT000417.1.fa_1 1371 1548 8471 8648 + 178 178 7278 2.71216e-109 - - - - - -
21----------
HT000442.1.fa_1 1947 2208 6404 6653 + 262 250 4707 2.99e-59 ACGA ACAA TG ACA TG ACA
22----------***
HT000461.1.fa_1 3339 3766 6466 6894 - 428 429 3556 1.8e-76 CTGCG CTGCG TGT ACA TGT ACA
23----------
HT001087.1.fa_1 40580 40999 51152 51573 + 420 422 10994 1.32e-87 - - - - - -
24----------
HT001108.1.fa_1 27414 28150 40006 40703 + 737 698 13290 1.512e-31 TACAA TACAT TG ACA TG ACA
25----------***
HT001164.1.fa_1 7608 8095 12410 12902 + 488 493 5295 7.6e-61 GATAT GATAT TGT ACA TGT ACA
26----------***
HT001193.1.fa_1 14835 15370 19889 20424 - 536 536 5590 7.8624e-98 ACAT ATAT TGT ACA TGT ACA
27----------***
HT001216.1.fa_1 9475 9741 14677 14943 + 267 267 5469 6.72e-104 ATAG ATAG TGT ACA TGT ACA
28----------
HT001239.1.fa_1 13378 13779 17992 18377 - 402 386 5000 5.822e-56 - - - - - -
10 changes: 10 additions & 0 deletions docs/source/sample/KH.rt.txt
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tmp-------------------------------------
I_HT001007.1.fa_359_1 R2 1.6e-18 5.7e-01
tmp-------------------------------------
L1_HT000162.1.fa_134792_2 L2 2.4e-10 1.1e-02
tmp-------------------------------------
R2_HT000615.1.fa_1124_2 R2 4.5e-31 1.7e-17
R2_HT000922.1.fa_1142_1 R1 3e-06 3.0e-09
tmp-------------------------------------
RTE_HT000680.1.fa_2312_1 L1 2.2e-53 2.9e-15
RTE_HT000798.1.fa_3113_2 - 1000 1.0e+00
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