BacBench
Collection
A multi-scale benchmark suite for bacterial genomics.
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13 items
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Updated
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1
Dataset Viewer
strain_name
string | contig_name
list | gene_name
list | locus_tag
list | start
list | end
list | strand
list | protein_id
list | protein_sequence
list | operon_prot_indices
list |
|---|---|---|---|---|---|---|---|---|---|
Escherichia coli
|
[
"NZ_CP026085.1"
] | [["dnaA","dnaN","recF","gyrB","yidB","yidA","yidX","dgoR","dgoK","dgoA","dgoD","dgoT","cbrA","yidR",(...TRUNCATED)
| [["C1467_RS00005","C1467_RS00010","C1467_RS00015","C1467_RS00020","C1467_RS00025","C1467_RS00030","C(...TRUNCATED)
| [[100,1508,2608,3710,6364,6877,7735,8669,9355,10217,10831,12054,13388,14553,15769,16407,16932,17557,(...TRUNCATED)
| [[1504,2609,3682,6125,6763,7690,8392,9359,10234,10835,11980,13392,14453,15768,16102,16821,17361,1921(...TRUNCATED)
| [[1,1,1,1,1,1,-1,1,1,1,1,1,-1,1,-1,1,1,1,-1,1,-1,1,1,-1,1,1,1,-1,1,-1,1,1,1,1,1,1,1,-1,1,1,1,-1,1,-1(...TRUNCATED)
| [["WP_000059111.1","WP_000673464.1","WP_000060112.1","WP_000072067.1","WP_000522208.1","WP_000985549(...TRUNCATED)
| [["MSLSLWQQCLARLQDELPATEFSMWIRPLQAELSDNTLALYAPNRFVLDWVRDKYLNNINGLLTSFCGADAPQLRFEVGTKPVTQTPQAAVTSNVAA(...TRUNCATED)
| [[[7,8],[76,77],[158,159],[357,358],[496,497],[515,516],[521,522],[732,733],[815,816],[927,928],[977(...TRUNCATED)
|
Mycobacterium tuberculosis H37Rv
|
[
"NC_000962.3"
] | [["dnaA","dnaN","recF",null,"gyrB","gyrA",null,null,"ppiA",null,null,null,"trpG","pknB","pknA","pbpA(...TRUNCATED)
| [["Rv0001","Rv0002","Rv0003","Rv0004","Rv0005","Rv0006","Rv0007","Rv0008c","Rv0009","Rv0010c","Rv001(...TRUNCATED)
| [[0,2051,3279,4433,5239,7301,9913,11873,12467,13132,13713,14088,14913,15589,17466,18758,20230,21636,(...TRUNCATED)
| [[1524,3260,4437,4997,7267,9818,10828,12311,13016,13558,13995,14877,15612,17470,18762,20234,21640,23(...TRUNCATED)
| [[1,1,1,1,1,1,1,-1,1,-1,-1,1,1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,1,1,1,1,1,1,1,1,1,1,1,-1,-1,1,-1,-1,1,-1(...TRUNCATED)
| [["NP_214515.1","NP_214516.1","NP_214517.1","NP_214518.1","NP_214519.2","NP_214520.1","NP_214521.1",(...TRUNCATED)
| [["MTDDPGSGFTTVWNAVVSELNGDPKVDDGPSSDANLSAPLTPQQRAWLNLVQPLTIVEGFALLSVPSSFVQNEIERHLRAPITDALSRRLGHQIQLG(...TRUNCATED)
| [[[111,112],[382,383],[390,391],[422,423],[456,457],[496,497],[845,846],[1046,1047],[1165,1166],[122(...TRUNCATED)
|
Mycobacteroides abscessus ATCC 19977
|
[
"NC_010397.1",
"NC_010394.1"
] | [["dnaA",null,"dnaN","gnd","recF",null,"gyrB",null,null,null,null,null,null,null,null,null,null,null(...TRUNCATED)
| [["MAB_RS00150","MAB_RS00155","MAB_RS00160","MAB_RS00165","MAB_RS00170","MAB_RS00175","MAB_RS00180",(...TRUNCATED)
| [[0,1552,2168,3418,4331,5472,6248,8408,9619,9896,10484,11716,12324,13079,14059,14300,14597,16689,172(...TRUNCATED)
| [[1476,1747,3368,4312,5480,6024,8276,9620,9847,10436,11699,12328,12723,13916,14284,14588,16145,17262(...TRUNCATED)
| [[1,-1,1,1,1,1,1,1,1,1,-1,-1,-1,-1,1,1,1,1,-1,1,1,-1,1,-1,1,1,-1,-1,-1,1,1,1,-1,-1,-1,-1,-1,-1,-1,1,(...TRUNCATED)
| [["WP_005079124.1","WP_005095934.1","WP_005064525.1","WP_005079128.1","WP_005112812.1","WP_005087667(...TRUNCATED)
| [["MTDELNSQFTAVWNTVVAELNGDDNQYLSSFPPLTPQQRAWLTLVKPLTMAEGFALLSVPSSFVQNEIERHLRGPIVEALSRRLGENVELGVRIAAP(...TRUNCATED)
| [[[48,49],[225,226],[289,290,291],[327,328],[730,731],[836,837],[1178,1179],[1196,1197],[1359,1360],(...TRUNCATED)
|
Pseudomonas aeruginosa PAO1
|
[
"NC_002516.2"
] | [["dnaA","dnaN","recF","gyrB","lptA",null,null,"glyS","glyQ","tag",null,null,null,null,null,"trkA",n(...TRUNCATED)
| [["PA0001","PA0002","PA0003","PA0004","PA0005","PA0006","PA0007","PA0008","PA0009","PA0010","PA0011"(...TRUNCATED)
| [[482,2055,3168,4274,7017,7802,8670,10433,12487,13539,14234,15206,15619,16334,16899,17365,18766,2006(...TRUNCATED)
| [[2027,3159,4278,6695,7791,8339,10377,12488,13435,14091,15122,15473,16273,16607,17217,18739,20071,21(...TRUNCATED)
| [[1,1,1,1,-1,-1,1,-1,-1,1,1,1,1,-1,-1,-1,-1,-1,-1,1,1,1,-1,1,1,1,1,1,-1,-1,-1,1,1,-1,-1,-1,-1,1,1,1,(...TRUNCATED)
| [["NP_064721.1","NP_064722.1","NP_064723.1","NP_064724.1","NP_064725.1","NP_064726.1","NP_064727.1",(...TRUNCATED)
| [["MSVELWQQCVDLLRDELPSQQFNTWIRPLQVEAEGDELRVYAPNRFVLDWVNEKYLGRLLELLGERGEGQLPALSLLIGSKRSRTPRAAIVPSQTHV(...TRUNCATED)
| [[[484,485],[604,605],[640,641],[1059,1060],[1066,1067],[1183,1184],[1190,1191],[1623,1624],[1650,16(...TRUNCATED)
|
Staphylococcus aureus subsp. aureus NCTC 8325
|
[
"NC_007795.1"
] | [["dnaA",null,null,"recF",null,null,null,null,null,null,null,null,null,null,"rplI",null,null,null,nu(...TRUNCATED)
| [["SAOUHSC_00001","SAOUHSC_00002","SAOUHSC_00003","SAOUHSC_00004","SAOUHSC_00005","SAOUHSC_00006","S(...TRUNCATED)
| [[516,2155,3669,3911,5033,7004,9754,10892,12785,14721,15413,16105,17364,18317,20281,20765,22443,2493(...TRUNCATED)
| [[1878,3289,3915,5024,6968,9668,10456,12407,14072,15417,15743,17074,18303,20285,20734,22166,23727,25(...TRUNCATED)
| [[1,1,1,1,1,1,-1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,-1,1,-1,1,1,-1,-1,-1,-1,1,1,1,-1,-1,1,1,-1,-1,1,-1,(...TRUNCATED)
| [["YP_498609.1","YP_498610.1","YP_498611.1","YP_498612.1","YP_498613.1","YP_498614.1","YP_498615.1",(...TRUNCATED)
| [["MSEKEIWEKVLEIAQEKLSAVSYSTFLKDTELYTIKDGEAIVLSSIPFNANWLNQQYAEIIQAILFDVVGYEVKPHFITTEELANYSNNETATPKET(...TRUNCATED)
| [[[50,51],[130,131],[161,162],[188,189],[209,210],[371,372,373],[388,389],[445,446],[455,456],[457,4(...TRUNCATED)
|
Dataset for operon identification from long-read RNA sequencing
A dataset of annotated operons across 5 distinct bacterial strains. The operons were annotated by running and analysing long-read RNA sequencing and identifying genes located on the same transcripts.
The genome protein sequences have been extracted from GenBank. Each row contains whole bacterial genome represented by an ordered list of protein sequences.
Usage
For a complete example on how to read and use the dataset, see Bacformer zero-shot operon prediction tutorial.
from datasets import load_dataset
dataset = load_dataset("macwiatrak/operon-identification-long-read-rna-sequencing", split="test")
# select a strain, here we will go for Mycobacterium tuberculosis (mtb)
mtb = dataset[1]
# select operons on the chromosome, mtb has no plasmids so there is only one contig (i.e. chromosome)
contig_idx = 0
chrom_operons = mtb['operon_prot_indices'][contig_idx]
# select the first operon
operon_prot_indices = chrom_operons[0]
print(operon_prot_indices)
# get protein sequences of the proteins belonging to the operon
operon_prot_seqs = [mtb['protein_sequence'][contig_idx][idx] for idx in operon_prot_indices]
operon_locus_tags = [mtb['locus_tag'][contig_idx][idx] for idx in operon_prot_indices]
See github repository for more details.
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Size of downloaded dataset files:
7.58 MB
Size of the auto-converted Parquet files:
7.58 MB
Number of rows:
5