Herve,

Is there a more elegant way to get all matched reference sequences besides using subject(matches)[start:end], e.g, subject(matches)[3010894 : 3010916] for each matched record? Thanks!
  23-letter "DNAString" instance
seq: GCGGAGCCTGAGGCAGAAACCTC

matches is the object returned by matchPattern function call.

matches
  Views on a 197195432-letter DNAString subject
subject: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...CCTATTCTAGTAAAAATTTTATTTCATTCTGTAAAGAATTTGGTATTAAACTTAAAACTGGAATTC
views:
           start       end width
   [1]   3010894   3010916    23 [GCGGAGCCTGAGGCAGAAACCTC]
   [2]   3299593   3299615    23 [GCTGTGGCTGAGATGAATACTGG]
   [3]   3637189   3637211    23 [CCTGCTTCTGCCTCTGCCACCGG]
   [4]   3660740   3660762    23 [GCTGTTGCTGCCGCTGTTGGTGG]
   [5]   3661169   3661191    23 [GCTGCCCCGGCCGCCGCCGCCCG]
   [6]   3661721   3661743    23 [CCCGCGGCTGCAGCACGAGCCGC]
....

Best regards,

Julie

 sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] BSgenome.Mmusculus.UCSC.mm9_1.3.19  BiocInstaller_1.10.3                REDseq_1.6.0
 [4] ChIPpeakAnno_2.8.0                  GenomicFeatures_1.12.3              limma_3.16.7
 [7] org.Hs.eg.db_2.9.0                  GO.db_2.9.0                         RSQLite_0.11.4
[10] DBI_0.2-7                           AnnotationDbi_1.22.6                BSgenome.Ecoli.NCBI.20080805_1.3.17
[13] biomaRt_2.16.0                      VennDiagram_1.6.5                   multtest_2.16.0
[16] Biobase_2.20.1                      BSgenome.Celegans.UCSC.ce2_1.3.19   BSgenome_1.28.0
[19] ShortRead_1.18.0                    latticeExtra_0.6-26                 RColorBrewer_1.0-5
[22] Rsamtools_1.12.4                    lattice_0.20-23                     Biostrings_2.28.0
[25] GenomicRanges_1.12.5                IRanges_1.18.3                      BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] bitops_1.0-6       hwriter_1.3        MASS_7.3-29        RCurl_1.95-4.1     rtracklayer_1.20.4 splines_3.0.1      stats4_3.0.1
 [8] survival_2.37-4    tools_3.0.1        XML_3.95-0.2       zlibbioc_1.6.0

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