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Extract founder (and reference) sequence from an alignment

Source: R/extract_seqs.R
extract_seqs.Rd

Extract founder (and reference) sequence from an alignment

Usage

extract_seqs(aln, founder_name, ref_name = NULL, start = 1, end = NULL)

Arguments

aln

alignment

founder_name

Name of founder sequence in the alignment

ref_name

Optional name of reference sequence in the alignment. This can be used as input to the ref_seq argument in run_wavess() (default: NULL, i.e. no reference sequence is returned)

start

start position in alignment

end

end position in alignment

Value

List of founder sequence and optional reference sequence as character strings

Examples

extract_seqs(hxb2_cons_founder, "B.US.2011.DEMB11US006.KC473833",
  start = 6225, end = 7787
)
#> $founder
#> [1] "ATGAGAGCGATGGGGATCATGAGGAATTGGCAACACTTGTGGAGATGGGGCATGATGCTCCTTGGGATGTTGATGATCTGTAATGCTACAGACAACTTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAGGGAAGCAAACACAACTCTATTTTGTGCATCAGATGCTAAAGCATATGAGACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAAAATTGGGAAATGTGACAGAAAATTTTAATGCATGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTCTATGGGATCAAAGCCTAAAGCCATGTGTAAGATTAACCCCACTCTGTGTTACTCTAAATTGCACTGATCTTAATGCCACTAGCATTGGTAGTAACATGACACTGAAGGGAGAAATAAAAAATTGCACTTTCAATATCACCACAAGTAAAAACGATAAAAAGACAACAGAACGTGCATATTTTAATAGACTTGATGTGGTACCAATGGATGATAATAGTAGTAGTAGTACTAGTTATAGGTTGATAAGTTGTAACACCTCAGTCATTACACATGCCTGCCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAAGTGTAATGATAAAAAATTTAATGGAAAAGGACTATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAGACCAGTAGTATCAACTCAACTGTTGCTGAATGGCAGTCTAGCAGAAGAAGAAGTAGTAATTAGATCTGAAAATATCTCTAACAATGCCAAAACCATAATAGTACATCTGAAGGAATCTGTACAAATTATTTGTGTAAGACCCAACAACAATACAAGACAAGGTATACATATGGGACCAGGAAGGACATTTTATACAACAGGGGGGATAATAGGAGATATAAGGCAAGCATATTGTAACATTAGTAGGGCAGAATGGACTAACACTCTAGGAAAGATAGTTGGAAAATTAAGAGAACGATTTAATAAAACAATAATCTTTAATCATTCCTCAGGAGGGGACCTAGAAATTGTGACACACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGCAATACATCAGCACTGTTTAATAGTACTTGGAATAGTACTATAAATACAAGTGAAAATGACACAATCATACTCCCATGCAGAATAAAACAAATTATAAATCTGTGGCAGGAAGTAGGAAGAGCAATGTATGCTCCTCCCATCAGGGGAAACATTAGCTGTACATCAAATATTACGGGGGTGCTATTAACAAGAGATGGTGGCGATGACCCTAACGGGACCAACGACACCGAGACCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAATGAATTGTATAAATACAAAGTAGTAAAAATTGAACCATTGGGAATAGCACCCACCAGGGCAAAGAGAAGAGTGGTGCAAAGAGAAAAAAGA"
#> 
#> $ref
#> NULL
#> 
extract_seqs(hxb2_cons_founder,
  "B.US.2011.DEMB11US006.KC473833", "B.FR.83.HXB2_LAI_IIIB_BRU.K03455",
  start = 6225, end = 7787
)
#> $founder
#> [1] "ATGAGAGCGATGGGGATCATGAGGAATTGGCAACACTTGTGGAGATGGGGCATGATGCTCCTTGGGATGTTGATGATCTGTAATGCTACAGACAACTTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAGGGAAGCAAACACAACTCTATTTTGTGCATCAGATGCTAAAGCATATGAGACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAAAATTGGGAAATGTGACAGAAAATTTTAATGCATGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTCTATGGGATCAAAGCCTAAAGCCATGTGTAAGATTAACCCCACTCTGTGTTACTCTAAATTGCACTGATCTTAATGCCACTAGCATTGGTAGTAACATGACACTGAAGGGAGAAATAAAAAATTGCACTTTCAATATCACCACAAGTAAAAACGATAAAAAGACAACAGAACGTGCATATTTTAATAGACTTGATGTGGTACCAATGGATGATAATAGTAGTAGTAGTACTAGTTATAGGTTGATAAGTTGTAACACCTCAGTCATTACACATGCCTGCCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAAGTGTAATGATAAAAAATTTAATGGAAAAGGACTATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAGACCAGTAGTATCAACTCAACTGTTGCTGAATGGCAGTCTAGCAGAAGAAGAAGTAGTAATTAGATCTGAAAATATCTCTAACAATGCCAAAACCATAATAGTACATCTGAAGGAATCTGTACAAATTATTTGTGTAAGACCCAACAACAATACAAGACAAGGTATACATATGGGACCAGGAAGGACATTTTATACAACAGGGGGGATAATAGGAGATATAAGGCAAGCATATTGTAACATTAGTAGGGCAGAATGGACTAACACTCTAGGAAAGATAGTTGGAAAATTAAGAGAACGATTTAATAAAACAATAATCTTTAATCATTCCTCAGGAGGGGACCTAGAAATTGTGACACACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGCAATACATCAGCACTGTTTAATAGTACTTGGAATAGTACTATAAATACAAGTGAAAATGACACAATCATACTCCCATGCAGAATAAAACAAATTATAAATCTGTGGCAGGAAGTAGGAAGAGCAATGTATGCTCCTCCCATCAGGGGAAACATTAGCTGTACATCAAATATTACGGGGGTGCTATTAACAAGAGATGGTGGCGATGACCCTAACGGGACCAACGACACCGAGACCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAATGAATTGTATAAATACAAAGTAGTAAAAATTGAACCATTGGGAATAGCACCCACCAGGGCAAAGAGAAGAGTGGTGCAAAGAGAAAAAAGA"
#> 
#> $ref
#> [1] "ATGAGAGTGAAGG---------AGAAATATCAGCACTTGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTTAATACCAATAGTAGTAGCGGGAGAATGATAATGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGA---------TACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATAGGACCAGGGAGAGCATTTGTTACAATAGGAAA---AATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAA------TAGCAAC---AATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGA"
#>