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igblastr 1.1.1: More built-in AIRR germline dbs for human
Add the following built-in germline dbs: _AIRR.human.IGH+IGK+IGL.202401 _AIRR.human.IGH+IGK+IGL.202401.src These were obtained from the following AIRR-community/OGRDB datasets: - IGH_VDJ: version 8 (released on 2024-01-11) - IGKappa_VJ: version 3 (released on 2024-01-11) - IGLambda_VJ: version 2 (released on 2024-01-11)
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‎DESCRIPTION‎

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biocViews: Immunology, Immunogenetics, ImmunoOncology, CellBiology
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URL: https://bioconductor.org/packages/igblastr
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BugReports: https://github.com/HyrienLab/igblastr/issues
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Version: 1.1.0
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Version: 1.1.1
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License: Artistic-2.0
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Encoding: UTF-8
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Authors@R: c(

‎inst/extdata/germline_sequences/AIRR/human/202309/README.md‎

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This folder contains germline sequences (in FASTA format) extracted from
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the following AIRR-community/OGRDB datasets for Human:
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- `IGH_VDJ` version 7
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- `IGKappa_VJ` version 2
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- `IGLambda_VJ` version 1
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- `IGH_VDJ`: version 7 (released on 2023-08-22)
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- `IGKappa_VJ`: version 2 (released on 2023-07-18)
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- `IGLambda_VJ`: version 1 (released on 2023-07-10)
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These were the most current versions at the date indicated by the name
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of this folder (202309 i.e. Sept 2023).

‎inst/extdata/germline_sequences/AIRR/human/202401/README.md‎

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This is the `extdata/germline_sequences/AIRR/human/202401/` folder
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in the **igblastr** package.
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This folder contains germline sequences (in FASTA format) extracted from
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the following AIRR-community/OGRDB datasets for Human:
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- `IGH_VDJ`: version 8 (released on 2024-01-11)
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- `IGKappa_VJ`: version 3 (released on 2024-01-11)
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- `IGLambda_VJ`: version 2 (released on 2024-01-11)
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These were the most current versions at the date indicated by the name
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of this folder (202401 i.e. Jan 2024).
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AIRR-community/OGRDB provides two flavors of each dataset, one called
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the "Reference Set" and the other one called the "Source Set". The `ref/`
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subfolder contains the former and `src/` the latter.
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See `README.md` file in each subfolder for more information.
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‎inst/extdata/germline_sequences/AIRR/human/202401/ref/IGHD.fasta‎

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>IGHD1-1*01
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GGTACAACTGGAACGAC
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>IGHD1-14*01
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GGTATAACCGGAACCAC
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>IGHD1-20*01
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GGTATAACTGGAACGAC
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>IGHD1-26*01
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GGTATAGTGGGAGCTACTAC
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>IGHD1-7*01
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GGTATAACTGGAACTAC
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>IGHD2-15*01
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AGGATATTGTAGTGGTGGTAGCTGCTACTCC
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>IGHD2-2*01
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AGGATATTGTAGTAGTACCAGCTGCTATGCC
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>IGHD2-2*02
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AGGATATTGTAGTAGTACCAGCTGCTATACC
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>IGHD2-21*01
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AGCATATTGTGGTGGTGATTGCTATTCC
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>IGHD2-21*02
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AGCATATTGTGGTGGTGACTGCTATTCC
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>IGHD2-8*01
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AGGATATTGTACTAATGGTGTATGCTATACC
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>IGHD2-8*02
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AGGATATTGTACTGGTGGTGTATGCTATACC
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>IGHD3-10*01
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GTATTACTATGGTTCGGGGAGTTATTATAAC
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>IGHD3-10*03
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GTATTACTATGGTTCAGGGAGTTATTATAAC
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>IGHD3-16*02
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GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC
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>IGHD3-16*03
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GTATTATGATTACATTTGGGGGAGTTATCGTTATACC
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>IGHD3-22*01
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GTATTACTATGATAGTAGTGGTTATTACTAC
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>IGHD3-3*01
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GTATTACGATTTTTGGAGTGGTTATTATACC
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>IGHD3-9*01
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GTATTACGATATTTTGACTGGTTATTATAAC
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>IGHD4-17*01
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TGACTACGGTGACTAC
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>IGHD4-23*01
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TGACTACGGTGGTAACTCC
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>IGHD4-4*01
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TGACTACAGTAACTAC
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>IGHD5-12*01
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GTGGATATAGTGGCTACGATTAC
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>IGHD5-18*02
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GTGAATATAGTGGCTACGATTAC
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>IGHD5-24*01
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GTAGAGATGGCTACAATTAC
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>IGHD5-5*01
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GTGGATACAGCTATGGTTAC
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>IGHD6-13*01
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GGGTATAGCAGCAGCTGGTAC
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>IGHD6-19*01
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GGGTATAGCAGTGGCTGGTAC
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>IGHD6-25*01
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GGGTATAGCAGCGGCTAC
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>IGHD6-6*01
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GAGTATAGCAGCTCGTCC
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>IGHD7-27*01
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CTAACTGGGGA

‎inst/extdata/germline_sequences/AIRR/human/202401/ref/IGHJ.fasta‎

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>IGHJ1*01
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GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
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>IGHJ2*01
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CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG
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>IGHJ3*02
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TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG
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>IGHJ4*02
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ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
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>IGHJ5*02
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ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
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>IGHJ6*02
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ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG
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>IGHJ6*03
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ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG

‎inst/extdata/germline_sequences/AIRR/human/202401/ref/IGHV.fasta‎

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‎inst/extdata/germline_sequences/AIRR/human/202401/ref/IGKJ.fasta‎

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>IGKJ1*01
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GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC
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>IGKJ2*01
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TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC
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>IGKJ2*03
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TGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC
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>IGKJ2*04
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TGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC
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>IGKJ3*01
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ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC
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>IGKJ4*01
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GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC
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>IGKJ5*01
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GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC

‎inst/extdata/germline_sequences/AIRR/human/202401/ref/IGKV.fasta‎

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‎inst/extdata/germline_sequences/AIRR/human/202401/ref/IGLJ.fasta‎

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>IGLJ1*01
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TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG
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>IGLJ2*01
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TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG
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>IGLJ3*02
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TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG
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>IGLJ4*01
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TTTTGTATTTGGTGGAGGAACCCAGCTGATCATTTTAG
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>IGLJ5*01
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CTGGGTGTTTGGTGAGGGGACCGAGCTGACCGTCCTAG
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>IGLJ5*02
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CTGGGTGTTTGGTGAGGGGACGGAGCTGACCGTCCTAG
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>IGLJ6*01
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TAATGTGTTCGGCAGTGGCACCAAGGTGACCGTCCTCG
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>IGLJ7*01
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TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGTCCTCG
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>IGLJ7*02
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TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGCCCTCG

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