Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Full genome sequences for Homo sapiens (GRCh38)DescriptionFull genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects. NoteThis BSgenome data package was made from the following source data files: GCA_000001405.15_GRCh38_top-level.fna.gz from ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38 See Author(s)The Bioconductor Dev Team See Also
Examples
BSgenome.Hsapiens.NCBI.GRCh38
genome <- BSgenome.Hsapiens.NCBI.GRCh38
seqlengths(genome)
genome[["1"]]
## ---------------------------------------------------------------------
## Genome-wide motif searching
## ---------------------------------------------------------------------
## See the GenomeSearching vignette in the BSgenome software
## package for some examples of genome-wide motif searching using
## Biostrings and the BSgenome data packages:
if (interactive())
vignette("GenomeSearching", package="BSgenome")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BSgenome.Hsapiens.NCBI.GRCh38)
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BSgenome.Hsapiens.NCBI.GRCh38/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BSgenome.Hsapiens.NCBI.GRCh38
> ### Title: Full genome sequences for Homo sapiens (GRCh38)
> ### Aliases: BSgenome.Hsapiens.NCBI.GRCh38-package
> ### BSgenome.Hsapiens.NCBI.GRCh38 Hsapiens
> ### Keywords: package data
>
> ### ** Examples
>
> BSgenome.Hsapiens.NCBI.GRCh38
Human genome:
# organism: Homo sapiens (Human)
# provider: NCBI
# provider version: GRCh38
# release date: 2013-12-17
# release name: Genome Reference Consortium Human Build 38
# 455 sequences:
# 1 2
# 3 4
# 5 6
# 7 8
# 9 10
# ... ...
# HSCHR19KIR_FH05_B_HAP_CTG3_1 HSCHR19KIR_FH06_A_HAP_CTG3_1
# HSCHR19KIR_FH06_BA1_HAP_CTG3_1 HSCHR19KIR_FH08_A_HAP_CTG3_1
# HSCHR19KIR_FH08_BAX_HAP_CTG3_1 HSCHR19KIR_FH13_A_HAP_CTG3_1
# HSCHR19KIR_FH13_BA2_HAP_CTG3_1 HSCHR19KIR_FH15_A_HAP_CTG3_1
# HSCHR19KIR_RP5_B_HAP_CTG3_1
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
# to access a given sequence)
> genome <- BSgenome.Hsapiens.NCBI.GRCh38
> seqlengths(genome)
1 2
248956422 242193529
3 4
198295559 190214555
5 6
181538259 170805979
7 8
159345973 145138636
9 10
138394717 133797422
11 12
135086622 133275309
13 14
114364328 107043718
15 16
101991189 90338345
17 18
83257441 80373285
19 20
58617616 64444167
21 22
46709983 50818468
X Y
156040895 57227415
MT HSCHR1_CTG1_UNLOCALIZED
16569 175055
HSCHR1_CTG2_UNLOCALIZED HSCHR1_CTG3_UNLOCALIZED
32032 127682
HSCHR1_CTG4_UNLOCALIZED HSCHR1_CTG5_UNLOCALIZED
66860 40176
HSCHR1_CTG6_UNLOCALIZED HSCHR1_CTG7_UNLOCALIZED
42210 176043
HSCHR1_CTG8_UNLOCALIZED HSCHR1_CTG9_UNLOCALIZED
40745 41717
HSCHR2_RANDOM_CTG1 HSCHR2_RANDOM_CTG2
161471 153799
HSCHR3UN_CTG2 HSCHR4_RANDOM_CTG4
155397 209709
HSCHR5_RANDOM_CTG1 HSCHR9_UNLOCALIZED_CTG1
92689 40062
HSCHR9_UNLOCALIZED_CTG2 HSCHR9_UNLOCALIZED_CTG3
38054 176845
HSCHR9_UNLOCALIZED_CTG4 HSCHR11_CTG1_UNLOCALIZED
39050 100316
HSCHR14_CTG1_UNLOCALIZED HSCHR14_CTG2_UNLOCALIZED
201709 211173
HSCHR14_CTG3_UNLOCALIZED HSCHR14_CTG4_UNLOCALIZED
194050 191469
HSCHR14_CTG5_UNLOCALIZED HSCHR14_CTG6_UNLOCALIZED
38115 39555
HSCHR14_CTG7_UNLOCALIZED HSCHR14_CTG8_UNLOCALIZED
172810 43739
HSCHR15_RANDOM_CTG1 HSCHR16_RANDOM_CTG1
448248 1872759
HSCHR17_RANDOM_CTG3 HSCHR17_RANDOM_CTG4
185591 280839
HSCHR17_RANDOM_CTG5 HSCHR22_UNLOCALIZED_CTG1
112551 150754
HSCHR22_UNLOCALIZED_CTG2 HSCHR22_UNLOCALIZED_CTG3
41543 179772
HSCHR22_UNLOCALIZED_CTG4 HSCHR22_UNLOCALIZED_CTG5
165050 42811
HSCHR22_UNLOCALIZED_CTG6 HSCHR22_UNLOCALIZED_CTG7
181920 103838
HSCHR22_UNLOCALIZED_CTG8 HSCHR22_UNLOCALIZED_CTG9
99375 73985
HSCHRY_RANDOM_CTG1 HSCHRUN_RANDOM_100
37240 2274
HSCHRUN_RANDOM_101 HSCHRUN_RANDOM_102
2165 1942
HSCHRUN_RANDOM_103 HSCHRUN_RANDOM_104
1472 21476
HSCHRUN_RANDOM_105 HSCHRUN_RANDOM_106
4416 1201
HSCHRUN_RANDOM_107 HSCHRUN_RANDOM_108
1444 2276
HSCHRUN_RANDOM_109 HSCHRUN_RANDOM_110
998 12399
HSCHRUN_RANDOM_111 HSCHRUN_RANDOM_112
37690 1179
HSCHRUN_RANDOM_113 HSCHRUN_RANDOM_114
2646 2489
HSCHRUN_RANDOM_115 HSCHRUN_RANDOM_116
1029 2145
HSCHRUN_RANDOM_117 HSCHRUN_RANDOM_118
2321 2140
HSCHRUN_RANDOM_119 HSCHRUN_RANDOM_120
2043 1445
HSCHRUN_RANDOM_121 HSCHRUN_RANDOM_122
981 1884
HSCHRUN_RANDOM_123 HSCHRUN_RANDOM_124
1361 392061
HSCHRUN_RANDOM_125 HSCHRUN_RANDOM_126
1233 1774
HSCHRUN_RANDOM_127 HSCHRUN_RANDOM_128
3920 92983
HSCHRUN_RANDOM_129 HSCHRUN_RANDOM_130
112505 4055
HSCHRUN_RANDOM_131 HSCHRUN_RANDOM_132
2415 2318
HSCHRUN_RANDOM_133 HSCHRUN_RANDOM_134
2186 1951
HSCHRUN_RANDOM_135 HSCHRUN_RANDOM_136
1300 22689
HSCHRUN_RANDOM_137 HSCHRUN_RANDOM_138
138126 5674
HSCHRUN_RANDOM_139 HSCHRUN_RANDOM_140
8127 6361
HSCHRUN_RANDOM_141 HSCHRUN_RANDOM_142
5353 3253
HSCHRUN_RANDOM_143 HSCHRUN_RANDOM_144
1899 2983
HSCHRUN_RANDOM_145 HSCHRUN_RANDOM_146
2168 993
HSCHRUN_RANDOM_147 HSCHRUN_RANDOM_148
91309 1202
HSCHRUN_RANDOM_149 HSCHRUN_RANDOM_154
1599 1400
HSCHRUN_RANDOM_155 HSCHRUN_RANDOM_156
2969 1553
HSCHRUN_RANDOM_157 HSCHRUN_RANDOM_158
7046 31033
HSCHRUN_RANDOM_159 HSCHRUN_RANDOM_160
44474 4685
HSCHRUN_RANDOM_161 HSCHRUN_RANDOM_162
4513 6504
HSCHRUN_RANDOM_163 HSCHRUN_RANDOM_164
6158 3041
HSCHRUN_RANDOM_165 HSCHRUN_RANDOM_166
5796 1652
HSCHRUN_RANDOM_167 HSCHRUN_RANDOM_168
1040 1368
HSCHRUN_RANDOM_169 HSCHRUN_RANDOM_170
2699 1048
HSCHRUN_RANDOM_171 HSCHRUN_RANDOM_172
1428 1428
HSCHRUN_RANDOM_173 HSCHRUN_RANDOM_174
1026 1121
HSCHRUN_RANDOM_175 HSCHRUN_RANDOM_176
1803 2855
HSCHRUN_RANDOM_177 HSCHRUN_RANDOM_178
3530 8320
HSCHRUN_RANDOM_179 HSCHRUN_RANDOM_180
1048 1045
HSCHRUN_RANDOM_181 HSCHRUN_RANDOM_182
1298 2387
HSCHRUN_RANDOM_183 HSCHRUN_RANDOM_184
1537 1143
HSCHRUN_RANDOM_185 HSCHRUN_RANDOM_186
1880 1216
HSCHRUN_RANDOM_187 HSCHRUN_RANDOM_188
970 1788
HSCHRUN_RANDOM_189 HSCHRUN_RANDOM_190
1484 1750
HSCHRUN_RANDOM_191 HSCHRUN_RANDOM_192
1308 1658
HSCHRUN_RANDOM_193 HSCHRUN_RANDOM_194
971 1930
HSCHRUN_RANDOM_195 HSCHRUN_RANDOM_196
990 4215
HSCHRUN_RANDOM_197 HSCHRUN_RANDOM_198
1136 2656
HSCHRUN_RANDOM_199 HSCHRUN_RANDOM_200
1650 1451
HSCHRUN_RANDOM_201 HSCHRUN_RANDOM_202
2378 2805
HSCHRUN_RANDOM_203 HSCHRUN_RANDOM_204
7992 7642
HSCHRUN_RANDOM_CTG1 HSCHRUN_RANDOM_CTG10
182896 179198
HSCHRUN_RANDOM_CTG11 HSCHRUN_RANDOM_CTG16
161802 179693
HSCHRUN_RANDOM_CTG17 HSCHRUN_RANDOM_CTG19
157432 15008
HSCHRUN_RANDOM_CTG2 HSCHRUN_RANDOM_CTG20
164239 210658
HSCHRUN_RANDOM_CTG21 HSCHRUN_RANDOM_CTG22
168472 41891
HSCHRUN_RANDOM_CTG23 HSCHRUN_RANDOM_CTG24
66486 198735
HSCHRUN_RANDOM_CTG25 HSCHRUN_RANDOM_CTG26
93321 158759
HSCHRUN_RANDOM_CTG27 HSCHRUN_RANDOM_CTG28
148850 150742
HSCHRUN_RANDOM_CTG29 HSCHRUN_RANDOM_CTG30
27745 62944
HSCHRUN_RANDOM_CTG33 HSCHRUN_RANDOM_CTG34
40191 36723
HSCHRUN_RANDOM_CTG35 HSCHRUN_RANDOM_CTG36
79590 71251
HSCHRUN_RANDOM_CTG4 HSCHRUN_RANDOM_CTG42
137718 186739
HSCHRUN_RANDOM_CTG6 HSCHRUN_RANDOM_CTG9
176608 161147
HSCHR1_1_CTG3 HSCHR1_2_CTG3
354444 256271
HSCHR1_1_CTG11 HSCHR1_4_CTG31
109528 185285
HSCHR1_1_CTG31 HSCHR1_2_CTG31
182439 110268
HSCHR1_3_CTG31 HSCHR1_4_CTG32_1
366580 50258
HSCHR1_3_CTG32_1 HSCHR1_1_CTG32_1
911658 425601
HSCHR1_2_CTG32_1 HSCHR2_2_CTG1
165834 136240
HSCHR2_3_CTG1 HSCHR2_4_CTG1
70887 223625
HSCHR2_1_CTG1 HSCHR2_1_CTG5
120616 143390
HSCHR2_1_CTG7 HSCHR2_5_CTG7_2
133041 138019
HSCHR2_4_CTG7_2 HSCHR2_3_CTG7_2
110395 110099
HSCHR2_2_CTG7_2 HSCHR2_1_CTG7_2
96131 123821
HSCHR2_3_CTG15 HSCHR2_1_CTG15
174166 161578
HSCHR3_1_CTG1 HSCHR3_3_CTG1
173151 109187
HSCHR3_4_CTG2_1 HSCHR3_1_CTG2_1
224108 180671
HSCHR3_2_CTG2_1 HSCHR3_3_CTG2_1
173649 248252
HSCHR3_5_CTG2_1 HSCHR3_1_CTG3
113034 205312
HSCHR3_2_CTG3 HSCHR3_9_CTG3
162429 184404
HSCHR4_1_CTG4 HSCHR4_1_CTG6
220246 376187
HSCHR4_1_CTG8_1 HSCHR4_1_CTG9
111943 586476
HSCHR4_4_CTG12 HSCHR4_1_CTG12
158965 164536
HSCHR4_2_CTG12 HSCHR4_5_CTG12
119912 205944
HSCHR4_3_CTG12 HSCHR5_5_CTG1
244096 126136
HSCHR5_4_CTG1 HSCHR5_3_CTG1
179043 195710
HSCHR5_1_CTG1 HSCHR5_2_CTG1
82728 226852
HSCHR5_6_CTG1 HSCHR5_2_CTG1_1
164558 1612928
HSCHR5_3_CTG1_1 HSCHR5_4_CTG1_1
101241 172708
HSCHR5_1_CTG5 HSCHR5_2_CTG5
173459 131892
HSCHR6_MHC_APD_CTG1 HSCHR6_1_CTG7
4672374 175808
HSCHR6_1_CTG6 HSCHR6_1_CTG2
152148 124736
HSCHR6_1_CTG8 HSCHR6_1_CTG9
870480 75005
HSCHR6_1_CTG3 HSCHR6_1_CTG4
185823 197536
HSCHR6_1_CTG5 HSCHR7_1_CTG1
271782 157952
HSCHR7_2_CTG4_4 HSCHR7_1_CTG4_4
209586 158166
HSCHR7_1_CTG6 HSCHR7_2_CTG6
119183 1111570
HSCHR7_3_CTG6 HSCHR7_2_CTG7
271455 126434
HSCHR7_1_CTG7 HSCHR8_4_CTG1
209988 145606
HSCHR8_2_CTG1 HSCHR8_1_CTG1
282736 292436
HSCHR8_8_CTG1 HSCHR8_3_CTG1
985506 300230
HSCHR8_9_CTG1 HSCHR8_1_CTG6
624492 141812
HSCHR8_1_CTG7 HSCHR8_5_CTG7
374415 133535
HSCHR8_6_CTG7 HSCHR8_4_CTG7
36640 158983
HSCHR8_3_CTG7 HSCHR8_2_CTG7
305841 132244
HSCHR9_1_CTG1 HSCHR9_1_CTG2
162988 71551
HSCHR9_1_CTG3 HSCHR9_1_CTG4
171286 60032
HSCHR9_1_CTG5 HSCHR10_1_CTG1
439082 179254
HSCHR10_1_CTG3 HSCHR10_1_CTG2
181496 309802
HSCHR10_1_CTG4 HSCHR11_1_CTG8
188315 210133
HSCHR11_1_CTG6 HSCHR11_1_CTG7
177092 296895
HSCHR11_1_CTG5 HSCHR11_1_CTG1_1
204059 154407
HG142_HG150_NOVEL_TEST HG151_NOVEL_TEST
200998 191409
HSCHR11_1_CTG3 HSCHR11_1_CTG2
67707 186169
HSCHR12_1_CTG1 HSCHR12_2_CTG2
167313 408271
HSCHR12_5_CTG2 HSCHR12_1_CTG2
40090 120804
HSCHR12_4_CTG2 HSCHR12_1_CTG2_1
238139 169178
HSCHR12_2_CTG2_1 HSCHR12_3_CTG2_1
138655 152874
HSCHR12_6_CTG2_1 HSCHR12_4_CTG2_1
119498 184319
HSCHR12_5_CTG2_1 HSCHR12_7_CTG2_1
76061 56134
HSCHR13_1_CTG3 HSCHR13_1_CTG2
191684 180306
HSCHR13_1_CTG6 HSCHR13_1_CTG4
103832 169134
HSCHR13_1_CTG1 HSCHR13_1_CTG5
306913 37287
HSCHR14_1_CTG1 HSCHR14_7_CTG1
322166 1511111
HSCHR14_2_CTG1 HSCHR14_3_CTG1
180703 1351393
HSCHR15_1_CTG1 HSCHR15_3_CTG3
478999 263054
HSCHR15_1_CTG3 HSCHR15_1_CTG8
327382 296527
HSCHR15_3_CTG8 HSCHR15_2_CTG8
244917 388773
HSCHR15_5_CTG8 HSCHR16_CTG2
430880 134193
HSCHR16_4_CTG1 HSCHR16_3_CTG1
63982 232857
HSCHR16_1_CTG1 HSCHR16_1_CTG3_1
2659700 192462
HSCHR16_2_CTG3_1 HSCHR17_1_CTG1
89672 375691
HSCHR17_2_CTG2 HSCHR17_1_CTG2
391357 196688
HSCHR17_7_CTG4 HSCHR17_4_CTG4
2877074 278131
HSCHR17_5_CTG4 HSCHR17_1_CTG4
70345 133151
HSCHR17_1_CTG5 HSCHR17_2_CTG4
1821992 223995
HSCHR17_8_CTG4 HSCHR17_9_CTG4
235827 108763
HSCHR17_3_CTG4 HSCHR17_1_CTG9
90219 178921
HSCHR18_4_CTG1_1 HSCHR18_1_CTG1_1
111737 289831
HSCHR18_2_CTG1_1 HSCHR18_2_CTG2
164789 198278
HSCHR18_1_CTG2 HSCHR18_1_CTG2_1
104552 167950
HSCHR18_2_CTG2_1 HSCHR18_3_CTG2_1
159547 167999
HSCHR19_5_CTG2 HSCHR19_4_CTG2
61734 52969
HSCHR19_1_CTG2 HSCHR19_2_CTG2
385657 170222
HSCHR19_3_CTG2 HSCHR19_1_CTG3_1
188024 155864
HSCHR19_2_CTG3_1 HSCHR19_3_CTG3_1
43156 233762
HSCHR19LRC_COX1_CTG3_1 HSCHR20_1_CTG1
987716 128386
HSCHR20_1_CTG2 HSCHR20_1_CTG4
118774 58661
HSCHR20_1_CTG3 HSCHR21_1_CTG1_1
183433 63917
HSCHR21_8_CTG1_1 HSCHR21_6_CTG1_1
166743 143900
HSCHR21_2_CTG1_1 HSCHR21_3_CTG1_1
201197 74653
HSCHR21_4_CTG1_1 HSCHR21_5_CTG2
116689 82692
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and