OMA results on reference1 of BAliBASE

This page summarizes the results of OMA on the reference1 subset of BAliBASE. These data sets do not contain more than eight sequences which makes them suitable as test sets for OMA. For more information on the data sets, see here.

Detailed information on each run is shown upon clicking on the name of the data set.
The detailed infomation includes

the resulting alignment
a table with information for each level of the iteration; note: a running time for each level is given: the sum over all levels is shorter then the total running time because there is some overall calculation that havbe to be done and is not counted for any level
a graph showing the progress of the iteration quality
a graph showing the performance of the algorithms

The entries with a yellow background are results we found especially interesting.

To view the data locally, it is possible to download all data sets in one file. (Note: This file is a slightly older version with some lines in the alignments missing.)

The tests were run on a

  % uname -a"
  SunOS q 5.6 Generic_105181-09 sun4u sparc SUNW,Ultra-Enterprise-10000

by Torsten Will, Technische Fakultät/FSPM, University of Bielefeld, Germany, June 13, 1999.

Explanation of the keys

Dataset	the underlying data set from BAliBASE
nSeq	number of sequences in the data set
lLen	length of the longest sequence
AvrIdent	average identity of the sequences (source: BAliBASE)
cost	the alignment cost that OMA found at the maximal dcaL. (Remember that for long sequences a higher dcaL may result in better costs, especially for runs that finished fast. It was not subject of this experiment to reach the "cost limit".)
max dcaL	value of dcaL in the last iteration step of OMA.
time[s]	the time usage of OMA. (Note for me: x.0!)
mem[8kb]	the memory used by OMA, measured in pages of 8kb each.

msa cost	cost that msa 2.1 computed. "not found" means that msa did not find an alignment within the given bounds. "?": msa exited abnormally, out of memory (2GB) or segmentation fault (crash); then no time can be given "*": not computed yet. Perhaps because of the bound of sequence length of 500
msa time	the time needed by MSA. If no time is given despite of "not found" the time is not recomputed yet (may follow). At an abnormal exit no time can be given.

test1 nSeq lLen AvrIdent cost max dcaL time[s] mem[8kb] msa cost msa time

1ajsA 4 384 ? 38470 128 2389.3 47683 not found

group 1

1aboA 5 80 15 10674 64 1343.8 45842 10708 199.2

1idy 5 58 14 9508 64 312.2 11703 9508 89.0

1r69 4 78 13 7294 64 27.7 1690 7308 7.9

1tvxA 4 69 18 6538 64 117.3 6531 6538 17.7

1ubi 4 94 18 8626 64 58.7 3670 8631 2.8

1wit 5 106 17 16517 64 152.1 4105 16517 10.9

2trx 4 99 17 9293 64 17.5 1542 9293 1.9

group 2

1aab 4 79 30 7061 32 5.8 841 7061 0.1

1fjlA 6 70 28 15973 64 6.1 972 not found

1hfh 5 132 31 19208 128 21.5 1139 19208 0.9

1hpi 4 81 33 6870 64 5.1 841 6870 0.3

1csy 5 104 30 16361 64 9.0 1104 ?

1pfc 5 117 28 17708 64 28.2 1338 17710 7.6

1tgxA 4 64 31 5695 64 4.8 839 5695 0.3

1ycc 4 116 29 10538 128 28.8 1915 10548 0.6

3cyr 4 109 31 9888 128 11.5 970 9888 0.6

451c 5 87 27 13364 64 277.2 6596 13380 8.8

group 3

1aho 5 67 44 9807 64 7.9 971 9807 0.4

1csp 5 70 51 9910 64 5.3 844 9910 0.1

1dox 4 96 46 8748 128 8.7 970 8748 0.6

1fkj 5 110 44 15809 64 6.6 1105 15809 0.3

1fmb 4 104 49 8804 64 5.8 970 8804 0.1

1krn 5 82 45 11409 64 6.3 973 11409 0.2

1plc 5 99 46 14205 128 9.0 975 14195 0.4

2fxb 5 63 51 8154 64 5.2 841 8154 0.1

2mhr 5 118 45 16687 64 6.5 1106 16687 0.3

9rnt 5 103 57 14475 64 6.7 976 14475 0.3

test2 nSeq lLen AvrIdent cost max dcaL time[s] mem[8kb] msa cost msa time

group 4

1bbt3 5 192 13 30730 128 2263.2 35447 ?

1sbp 5 263 19 43149 64 >9000 ? not found

1havA 5 199 15 31928 32 >9000 ? not found 339370.0

1uky 4 220 15 21112 64 >18000 ? ?

2hsdA 4 262 19 25281 128 151.4 5856 not found 89.2

2pia 4 287 20 26618 64 171.7 5815 not found 685.5

3grs 4 237 14 23478 128 97.7 3785 not found 185.8

kinase 5 276 20 46064 128 121.5 3800 not found 19421.5

group 5

1ad2 4 213 30 19714 128 20.0 1301 19714 2.3

1aym3 4 244 32 22031 128 16.3 1110 22031 9.9

1gdoA 4 265 30 24082 128 31.7 1441 24082 100.6

1ldg 4 315 27 29939 128 18.0 1110 29939 4.0

1mrj 4 266 33 24165 128 19.0 1112 24157 4.8

1pgtA 4 212 26 20160 128 24.7 1630 20160 5.5

1pii 4 259 32 24362 128 15.7 1113 24347 5.9

1ton 5 244 30 37911 128 1269.9 25899 not found 3205.0

2cba 5 259 26 40281 128 2342.4 27580 not found 3205.0

group 6

1amk 5 254 49 36659 128 19.1 1155

1ar5A 4 203 42 17722 128 16.3 979 17722 0.7

1bco 5 200 11 29538 64 >9000 ? ?

1ezm 5 308 60 43746 128 22.0 1299 43746 2.4

1led 4 243 43 21788 128 15.7 983 21788 1.9

1ppn 5 220 46 31731 128 15.5 1730 31731 1.4

1pysA 4 266 44 22586 128 15.7 1113 22586 1.1

1thm 4 279 49 24978 128 16.5 1113 24978 1.2

1tis 5 295 50 41462 128 20.0 1246 41462 3.1

1zin 4 216 42 19220 128 11.0 1312 *

5ptp 5 245 43 34752 128 17.0 1121 34762 1.5

test3 nSeq lLen AvrIdent cost max dcaL time[s] mem[8kb] msa cost msa time

group 7

1ajsA 4 387 15 38473 128 2505.5 49436 not found 1458.1

1cpt 4 434 20 39908 128 37.7 1221 *

1lvl 4 449 19 44148 128 6619.0 153585 *

1pamA 5 572 18 86482 32 >15000 ? *

1ped 3 374 24 17908 128 28.1 1608 *

2myr 4 474 16 43532 128 1941.7 52676 *

4enl 3 421 20 18936 128 26.2 1292 *

gal4 5 395 14 62763 128 4376.0 44617 *

group 8

1ac5 4 483 29 43341 128 235.7 11446 not found 524.6

1adj 4 418 35 38051 128 23.7 1319 38036 3.1

1bgl 4 993 31 90863 128 69.3 1408 *

1dlc 4 590 32 54960 128 140.6 6020 *

1eft 4 405 30 36622 128 42.4 1739 *

1fieA 4 675 34 61586 128 39.1 1432 *

1gowA 4 481 31 45328 128 102.3 3246 *

1pkm 4 449 34 42100 128 31.2 1130 *

1sesA 5 442 33 67150 128 57.3 1876 *

2ack 5 482 28 77137 128 2085.9 29418 *

arp 5 418 29 64154 128 612.6 11608 *

glg 5 486 31 74397 128 219.0 4626 *

group 9

1ad3 4 447 47 39218 128 24.3 1413 39209 3.6

1gpb 5 828 47 117934 128 56.9 1886 *

1gtr 5 436 42 64202 128 35.6 1213 *

1lcf 6 691 49 149517 128 3613.1 30020 *

1rthA 5 541 42 80352 128 41.6 1399 *

1taq 5 928 40 133901 128 7152.0 99398 *

3lad 4 471 ? 45205 128 33.7 1132 *

3pmg 4 567 51 49121 128 37.0 1140 *

actin 5 395 45 56940 128 26.0 1748 *

Dataset nSeq lLen AvrIdent cost max dcaL time[s] mem[8kb] msa cost msa time