Biostrings

See http://www.bioconductor.org/packages/2.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

library(BSgenome.Hsapiens.UCSC.hg19)

What are the chr names?

seqnames(Hsapiens)

##  [1] "chr1"                  "chr2"                 
##  [3] "chr3"                  "chr4"                 
##  [5] "chr5"                  "chr6"                 
##  [7] "chr7"                  "chr8"                 
##  [9] "chr9"                  "chr10"                
## [11] "chr11"                 "chr12"                
## [13] "chr13"                 "chr14"                
## [15] "chr15"                 "chr16"                
## [17] "chr17"                 "chr18"                
## [19] "chr19"                 "chr20"                
## [21] "chr21"                 "chr22"                
## [23] "chrX"                  "chrY"                 
## [25] "chrM"                  "chr1_gl000191_random" 
## [27] "chr1_gl000192_random"  "chr4_ctg9_hap1"       
## [29] "chr4_gl000193_random"  "chr4_gl000194_random" 
## [31] "chr6_apd_hap1"         "chr6_cox_hap2"        
## [33] "chr6_dbb_hap3"         "chr6_mann_hap4"       
## [35] "chr6_mcf_hap5"         "chr6_qbl_hap6"        
## [37] "chr6_ssto_hap7"        "chr7_gl000195_random" 
## [39] "chr8_gl000196_random"  "chr8_gl000197_random" 
## [41] "chr9_gl000198_random"  "chr9_gl000199_random" 
## [43] "chr9_gl000200_random"  "chr9_gl000201_random" 
## [45] "chr11_gl000202_random" "chr17_ctg5_hap1"      
## [47] "chr17_gl000203_random" "chr17_gl000204_random"
## [49] "chr17_gl000205_random" "chr17_gl000206_random"
## [51] "chr18_gl000207_random" "chr19_gl000208_random"
## [53] "chr19_gl000209_random" "chr21_gl000210_random"
## [55] "chrUn_gl000211"        "chrUn_gl000212"       
## [57] "chrUn_gl000213"        "chrUn_gl000214"       
## [59] "chrUn_gl000215"        "chrUn_gl000216"       
## [61] "chrUn_gl000217"        "chrUn_gl000218"       
## [63] "chrUn_gl000219"        "chrUn_gl000220"       
## [65] "chrUn_gl000221"        "chrUn_gl000222"       
## [67] "chrUn_gl000223"        "chrUn_gl000224"       
## [69] "chrUn_gl000225"        "chrUn_gl000226"       
## [71] "chrUn_gl000227"        "chrUn_gl000228"       
## [73] "chrUn_gl000229"        "chrUn_gl000230"       
## [75] "chrUn_gl000231"        "chrUn_gl000232"       
## [77] "chrUn_gl000233"        "chrUn_gl000234"       
## [79] "chrUn_gl000235"        "chrUn_gl000236"       
## [81] "chrUn_gl000237"        "chrUn_gl000238"       
## [83] "chrUn_gl000239"        "chrUn_gl000240"       
## [85] "chrUn_gl000241"        "chrUn_gl000242"       
## [87] "chrUn_gl000243"        "chrUn_gl000244"       
## [89] "chrUn_gl000245"        "chrUn_gl000246"       
## [91] "chrUn_gl000247"        "chrUn_gl000248"       
## [93] "chrUn_gl000249"

Try getting a pattern

matchPattern("ACCCAGGGC", Hsapiens$chr22, max.mismatch=0)

##   Views on a 51304566-letter DNAString subject
## subject: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
## views:
##          start      end width
##   [1] 16073483 16073491     9 [ACCCAGGGC]
##   [2] 16088026 16088034     9 [ACCCAGGGC]
##   [3] 17454954 17454962     9 [ACCCAGGGC]
##   [4] 17598069 17598077     9 [ACCCAGGGC]
##   [5] 17716824 17716832     9 [ACCCAGGGC]
##   ...      ...      ...   ... ...
## [433] 50908633 50908641     9 [ACCCAGGGC]
## [434] 50912572 50912580     9 [ACCCAGGGC]
## [435] 50925808 50925816     9 [ACCCAGGGC]
## [436] 50940971 50940979     9 [ACCCAGGGC]
## [437] 50997332 50997340     9 [ACCCAGGGC]

Loop through. E.g.,

paste0("chr", c(1:22, "X", "Y"))

##  [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8" 
##  [9] "chr9"  "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16"
## [17] "chr17" "chr18" "chr19" "chr20" "chr21" "chr22" "chrX"  "chrY"

See See http://www.bioconductor.org/packages/2.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf for more.