R/align_lineage.R
repAlignLineage.RdThis function aligns all sequences (incliding germline) that belong to one clonal lineage and one cluster. After clustering and building the clonal lineage and germline, the next step is to analyze the degree of mutation and maturity of each clonal lineage. This allows for finding high mature cells and cells with a large number of offspring. The phylogenetic analysis will find mutations that increase the affinity of BCR. Making alignment of the sequence is the first step towards sequence analysis including BCR.
repAlignLineage(.data, .min_lineage_sequences, .prepare_threads, .align_threads, .nofail)The data to be processed. Can be data.frame, data.table or a list of these objects.
If number of sequences in the same clonal lineage and the same cluster (not including germline) is lower than this threshold, this group of sequences will be filtered out from the dataframe; so only large enough lineages will be included.
Number of threads to prepare results table. Please note that high number can cause heavy memory usage!
Number of threads for lineage alignment.
It must have columns in the immunarch compatible format immunarch_data_format, and also must contain 'Cluster' column, which is added by seqCluster() function, and 'Germline.sequence' column, which is added by repGermline() function.
Will return NA instead of stopping if Clustal W is not installed. Used to avoid raising errors in examples on computers where Clustal W is not installed.
Dataframe or list of dataframes (if input is a list with multiple samples). The dataframe has these columns: * Cluster: cluster name * Germline: germline sequence * Alignment: DNAbin object with alignment * Sequences: nested dataframe containing all sequences for this combination of cluster and germline; it has columns * Sequence, CDR1.nt, CDR2.nt, CDR3.nt, FR1.nt, FR2.nt, FR3.nt, FR4.nt, V.allele, J.allele, V.aa, J.aa: all values taken from the input dataframe * Clone.ID: taken from the input dataframe, or created (filled with row numbers) if missing * Clones: taken from the input dataframe, or created (filled with '1' values) if missing
data(bcrdata)
bcr_data <- bcrdata$data
bcr_data %>%
seqCluster(seqDist(bcr_data), .fixed_threshold = 3) %>%
repGermline(.threads = 1) %>%
repAlignLineage(.min_lineage_sequences = 2, .align_threads = 2, .nofail = TRUE)
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `length_value = map_chr(.y, ~ifelse(all(.x == .x[1]), yes =
#> .x[1], no = glue("range_{min(.x)}:{max(.x)}")))`.
#> Caused by warning:
#> ! Automatic coercion from integer to character was deprecated in purrr 1.0.0.
#> ℹ Please use an explicit call to `as.character()` within `map_chr()` instead.
#> ℹ The deprecated feature was likely used in the immunarch package.
#> Please report the issue at <https://github.com/immunomind/immunarch/issues>.
#> Warning: Genes or alleles IGHV4-55 from sample full_clones not found in the reference and will be dropped!
#> Probably, species argument is wrong (current value: HomoSapiens) or the data contains non-BCR genes.
#> $full_clones
#> Cluster
#> 1 IGHV4-61/IGHJ4_length_45_cluster_1
#> 2 IGHV4-61/IGHJ4_length_63_cluster_1
#> 3 IGHV5-51/IGHJ4_length_60_cluster_1
#> 4 IGHV5-51/IGHJ5_length_45_cluster_1
#> Germline
#> 1 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 2 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 3 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 4 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> Alignment
#> 1 c, c, c, a, a, a, g, g, g, g, g, g, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, c, c, c, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, g, g, g, a, a, a, g, g, g, t, t, t, c, c, c, g, g, g, g, g, g, g, g, g, c, c, c, c, c, c, c, c, c, a, a, a, g, g, g, g, g, g, a, a, a, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, g, g, g, a, a, a, a, a, a, g, g, g, c, c, c, c, c, c, t, t, t, t, t, t, c, c, c, g, g, g, g, g, g, a, a, a, g, g, g, a, a, a, c, c, c, c, c, c, c, c, c, t, t, t, g, g, g, t, t, t, c, c, c, c, c, c, c, c, c, t, t, t, c, c, c, a, a, a, c, c, c, c, c, c, t, t, t, g, g, g, c, c, c, a, a, a, c, c, c, t, t, t, g, g, g, t, t, t, c, c, c, t, t, t, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, g, g, g, g, g, g, c, c, c, t, t, t, c, c, c, c, c, c, g, g, g, t, t, t, c, c, c, a, a, a, g, g, g, c, c, c, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, t, t, t, a, g, g, g, g, g, t, t, t, t, t, t, a, a, a, c, c, c, t, t, t, a, a, a, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, g, g, g, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, t, t, t, c, c, c, c, c, c, g, g, g, g, g, g, c, c, c, a, a, a, g, g, g, c, c, c, c, c, c, c, c, c, c, c, c, c, c, c, a, a, a, g, g, g, g, g, g, g, g, g, a, a, a, a, a, a, g, g, g, g, g, g, g, g, g, a, a, a, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, a, a, a, t, t, t, t, t, t, g, g, g, g, g, g, g, g, a, t, t, t, a, a, a, t, t, t, a, g, a, t, t, t, c, c, t, t, c, c, a, a, a, t, t, t, t, c, t, a, a, a, c, c, c, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, g, g, g, a, a, a, g, g, a, c, c, c, a, a, t, c, c, c, c, c, c, a, a, t, a, a, t, c, t, c, t, t, t, a, a, a, c, c, c, a, a, a, a, a, a, c, t, c, c, c, c, c, c, c, c, c, c, t, t, t, c, c, c, c, c, c, c, c, c, t, t, t, c, c, c, a, a, a, a, a, a, g, g, a, a, c, a, g, g, g, t, t, t, c, c, c, g, g, g, a, a, a, g, g, g, t, t, t, c, c, c, a, a, a, c, c, c, c, c, c, a, a, a, t, t, t, a, g, g, t, t, t, c, c, c, a, a, a, g, g, g, t, t, t, a, a, a, g, g, g, a, a, a, c, c, c, a, a, a, c, c, c, g, g, g, t, g, t, c, c, c, c, c, c, a, a, a, a, g, a, g, g, g, a, a, a, a, a, a, c, g, c, c, c, c, a, a, a, g, g, g, t, t, t, t, t, t, c, g, c, t, t, t, c, c, c, c, c, c, c, c, c, t, t, t, g, g, g, a, a, a, a, a, g, g, a, g, c, t, t, t, t, t, g, g, g, a, a, a, g, c, c, c, c, c, t, t, t, c, c, c, t, t, t, g, g, g, t, t, t, g, g, g, a, a, a, c, c, c, c, c, c, g, g, g, c, c, c, t, t, t, g, g, g, c, c, c, g, g, g, g, g, g, a, a, a, c, c, c, a, a, a, c, c, c, g, g, g, g, g, g, c, c, c, c, c, c, g, g, g, t, t, t, g, g, g, t, t, t, a, a, a, t, t, t, t, t, t, a, t, t, c, c, c, n, t, t, n, g, g, n, t, t, n, g, g, n, c, c, n, g, g, n, a, a, n, g, g, n, a, a, n, g, g, n, g, g, n, c, c, n, g, g, n, c, c, n, c, c, n, g, g, n, g, g, n, g, g, n, g, g, n, a, a, n, c, c, n, t, t, n, a, a, n, c, c, n, a, g, n, g, c, n, c, c, n, a, a, n, c, c, n, t, t, n, c, c, n, c, c, n, c, c, n, t, t, n, t, t, n, t, t, n, g, g, n, a, a, n, c, c, n, t, t, n, a, a, n, c, c, n, t, t, n, g, g, n, g, g, g, g, g, g, g, g, c, c, c, c, c, c, a, a, c, a, g, g, g, g, g, g, g, g, a, a, a, a, g, a, c, c, c, c, c, c, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, c, c, c, a, a, a, c, c, c, c, c, c, g, g, g, t, t, t, c, c, c, t, t, t, c, c, c, c, c, c, t, t, t, c, c, c, a, a, a, g, g, g
#> 2 c, c, c, a, a, a, g, g, g, g, g, g, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, c, c, c, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, g, g, g, a, a, a, g, g, g, t, t, t, c, c, c, g, g, g, g, g, g, g, g, g, c, c, c, c, c, c, c, c, c, a, a, a, g, g, g, g, g, g, a, a, a, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, g, g, g, a, a, a, a, a, a, g, g, g, c, c, c, c, c, c, t, t, t, t, t, t, c, c, c, g, g, g, g, g, g, a, a, a, g, g, g, a, a, a, c, c, c, c, c, c, c, c, c, t, t, t, g, g, g, t, t, t, c, c, c, c, c, c, c, c, c, t, t, t, c, c, c, a, a, a, c, c, c, c, c, c, t, t, t, g, g, g, c, c, c, a, a, a, c, c, c, t, t, t, g, g, g, t, t, t, c, c, c, t, t, t, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, g, g, g, g, g, g, c, c, c, t, t, t, c, c, c, c, c, c, g, g, g, t, t, t, c, c, c, a, a, a, g, g, g, c, c, c, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, t, t, t, a, g, g, g, g, g, t, t, t, t, t, t, a, a, a, c, c, c, t, t, t, a, a, a, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, g, g, g, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, t, t, t, c, c, c, c, c, c, g, g, g, g, g, g, c, c, c, a, a, a, g, g, g, c, c, c, c, c, c, c, c, c, c, c, c, c, c, c, a, a, a, g, g, g, g, g, g, g, g, g, a, a, a, a, a, a, g, g, g, g, g, g, g, g, g, a, a, a, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, a, a, a, t, t, t, t, t, t, g, g, g, g, g, g, g, g, g, t, t, a, a, a, a, t, t, t, a, a, a, t, t, t, c, c, c, t, t, t, a, a, a, t, t, t, t, t, t, a, a, a, c, c, c, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, g, g, g, a, a, a, g, g, c, c, t, t, a, a, a, c, c, c, c, c, c, a, a, a, a, a, a, c, c, c, t, t, t, a, a, a, c, c, c, a, a, a, a, a, a, c, c, c, c, c, c, c, c, c, c, c, c, t, t, t, c, c, c, c, c, c, c, c, c, t, t, t, c, c, c, a, a, a, a, a, a, g, g, g, a, a, a, g, g, g, t, t, t, c, c, c, g, g, g, a, a, a, g, g, g, t, t, t, c, c, c, a, a, a, c, g, g, c, c, c, a, a, a, t, t, t, a, a, a, t, t, t, c, c, c, a, a, c, g, t, t, t, t, t, a, a, a, g, g, g, a, a, a, c, c, c, a, a, a, c, c, c, g, g, g, t, t, t, c, c, c, c, c, c, a, a, a, a, a, a, g, g, g, a, a, a, a, a, a, c, c, c, c, c, c, a, a, a, g, g, g, t, t, t, t, t, t, c, c, c, t, t, t, c, c, c, c, c, c, c, c, c, t, t, t, g, g, g, a, a, a, a, a, c, g, c, c, c, c, c, t, t, t, g, g, g, a, a, a, g, g, g, c, c, g, t, t, t, c, c, c, t, t, t, g, g, g, t, t, t, g, g, g, a, a, a, c, c, c, c, c, c, g, g, g, c, c, c, t, t, t, g, g, g, c, c, c, g, g, g, g, g, g, a, a, a, c, c, c, a, a, a, c, c, c, g, g, g, g, g, g, c, c, c, c, c, c, g, g, g, t, t, t, g, g, g, t, t, t, a, a, a, t, t, t, t, t, t, a, t, t, c, t, t, n, t, t, n, g, g, n, t, t, n, g, g, n, c, c, n, g, g, n, a, a, n, g, g, n, a, a, n, g, g, n, a, a, n, t, t, n, c, c, n, a, a, n, t, t, n, c, c, n, a, a, n, c, c, n, a, a, n, g, g, n, t, t, n, t, t, n, t, t, n, c, c, n, t, t, n, a, a, n, t, t, n, g, g, n, a, a, n, t, t, n, a, a, n, c, c, n, t, a, n, a, a, n, g, g, n, t, t, n, g, g, n, g, g, n, t, t, n, t, t, n, a, a, n, t, t, n, t, t, n, a, a, n, t, t, n, c, c, n, c, c, n, c, c, n, t, t, n, a, a, n, c, c, n, t, t, n, t, t, n, t, t, n, g, g, n, a, a, n, c, c, n, t, t, n, a, a, n, c, c, n, t, t, n, g, g, n, g, g, g, g, g, g, g, g, c, c, c, c, c, c, a, a, a, a, g, g, g, g, g, g, g, g, a, a, a, a, a, a, c, c, c, c, c, c, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, c, c, c, a, a, a, c, c, c, c, c, c, g, g, g, t, t, t, c, c, c, t, t, t, c, c, c, c, c, c, t, t, t, c, c, c, a, a, a, g, g, g
#> 3 g, g, g, a, a, a, g, g, g, g, g, g, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, t, t, t, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, g, g, g, c, c, c, a, a, a, g, g, g, a, a, a, g, g, g, g, g, g, t, t, t, g, g, g, a, a, a, a, a, a, a, a, a, a, a, a, a, a, a, g, g, g, c, c, c, c, c, c, c, c, c, g, g, g, g, g, g, g, g, g, g, g, g, a, a, a, g, g, g, t, t, t, c, c, c, t, t, t, c, c, c, t, t, t, g, g, g, a, a, a, a, a, a, g, g, g, a, a, a, t, t, t, c, c, c, t, t, t, c, c, c, c, c, c, t, t, t, g, g, g, t, t, t, a, a, a, a, a, a, g, g, g, g, g, g, g, g, g, t, t, t, t, t, t, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, t, t, t, a, a, a, c, c, c, a, a, a, g, g, g, c, c, c, t, t, t, t, t, t, t, t, t, a, a, a, c, c, c, c, c, c, a, a, a, g, g, g, c, c, c, t, t, t, a, a, a, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, t, t, t, c, c, c, g, g, g, g, g, g, c, c, c, t, t, t, g, g, g, g, g, g, g, g, g, t, t, t, g, g, g, c, c, c, g, g, g, c, c, c, c, c, c, a, a, a, g, g, g, a, a, a, t, t, t, g, g, g, c, c, c, c, c, c, c, c, c, g, g, g, g, g, g, g, g, g, a, a, a, a, a, a, a, a, a, g, g, g, g, g, g, c, c, c, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, a, a, a, t, t, t, g, g, g, g, g, g, g, g, g, g, g, a, a, a, a, t, t, t, c, c, c, a, a, a, t, t, t, c, c, c, t, t, t, a, a, a, t, t, t, c, c, c, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, g, g, g, a, a, a, c, c, c, t, t, t, c, c, c, t, t, t, g, g, g, a, a, a, t, t, t, a, a, a, c, c, c, c, c, c, a, a, a, g, g, g, a, a, a, t, t, t, a, a, a, c, c, c, a, a, a, g, g, g, c, c, c, c, c, c, c, c, c, g, g, g, t, t, t, c, c, c, c, c, c, t, t, t, t, t, t, c, c, c, c, c, c, a, a, a, a, a, a, g, g, g, g, a, a, c, c, c, c, c, c, a, a, a, g, g, g, g, g, g, t, t, t, c, c, c, a, a, a, c, c, g, c, c, c, a, a, a, t, t, t, c, g, g, t, t, t, c, c, c, a, a, a, g, g, g, c, t, t, c, c, c, g, g, g, a, g, g, c, c, c, a, a, a, a, a, a, g, g, g, t, t, t, c, c, c, c, c, c, a, a, a, t, t, t, c, c, c, a, g, g, g, g, g, c, c, c, a, a, a, c, c, c, c, c, c, g, g, g, c, c, c, c, c, c, t, t, t, a, a, a, c, c, c, c, c, c, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, a, a, a, g, g, g, c, c, c, a, a, a, g, g, g, c, c, c, c, c, c, t, t, t, g, g, g, a, a, a, a, a, a, g, g, g, g, g, g, c, c, c, c, c, c, t, t, t, c, c, c, g, g, g, g, g, g, a, a, a, c, c, c, a, a, a, c, c, c, c, c, c, g, g, g, c, c, c, c, c, c, a, a, a, t, t, t, g, g, g, t, t, t, a, a, a, t, t, t, t, t, t, a, a, a, c, c, c, n, t, t, n, g, g, n, t, t, n, g, g, n, t, t, n, g, a, n, a, a, n, g, g, n, a, a, n, c, c, n, a, a, n, c, c, n, t, t, n, c, c, n, t, t, n, g, g, n, g, g, n, t, t, n, a, a, n, a, a, n, g, g, n, a, a, n, t, t, n, a, a, n, g, g, n, a, a, n, a, a, n, t, t, n, c, c, n, a, a, n, t, t, n, c, c, n, t, t, n, g, g, n, t, t, n, g, g, n, g, g, n, g, g, n, c, c, n, c, c, n, c, c, n, c, c, n, a, a, n, g, g, n, a, a, n, a, a, n, g, c, n, c, c, n, t, t, n, t, t, n, t, t, n, g, g, n, a, a, n, c, c, n, t, t, n, a, a, n, c, c, n, t, t, n, g, g, n, g, g, g, g, g, g, g, g, c, c, c, c, c, c, a, a, a, a, g, g, g, g, g, g, g, g, a, a, a, a, a, a, c, c, c, c, c, c, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, c, c, c, a, a, a, c, c, c, c, c, c, g, g, g, t, t, t, c, c, c, t, t, t, c, c, c, c, c, c, t, t, t, c, c, c, a, a, a, g, g, g
#> 4 g, g, g, a, a, a, g, g, g, g, g, g, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, t, t, t, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, g, g, g, c, c, c, a, a, a, g, g, g, a, a, a, g, g, g, g, g, g, t, t, t, g, g, g, a, a, a, a, a, a, a, a, a, a, a, a, a, a, a, g, g, g, c, c, c, c, c, c, c, c, c, g, g, g, g, g, g, g, g, g, g, g, g, a, a, a, g, g, g, t, t, t, c, c, c, t, t, t, c, c, c, t, t, t, g, g, g, a, a, a, a, a, a, g, g, g, a, a, a, t, t, t, c, c, c, t, t, t, c, c, c, c, c, c, t, t, t, g, g, g, t, t, t, a, a, a, a, a, a, g, g, g, g, g, g, g, g, g, t, t, t, t, t, t, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, t, t, t, a, a, a, c, c, c, a, a, a, g, g, g, c, c, c, t, t, t, t, t, t, t, t, t, a, a, a, c, c, c, c, c, c, a, a, a, g, g, g, c, c, c, t, t, t, a, a, a, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, t, t, t, c, c, c, g, g, g, g, g, g, c, c, c, t, t, t, g, g, g, g, g, g, g, g, g, t, t, t, g, g, g, c, c, c, g, g, g, c, c, c, c, c, c, a, a, a, g, g, g, a, a, a, t, t, t, g, g, g, c, c, c, c, c, c, c, c, c, g, g, g, g, g, g, g, a, g, a, a, a, a, a, a, a, a, a, g, g, g, g, g, g, c, c, c, c, c, c, t, t, t, g, g, g, g, g, g, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, a, g, t, t, t, t, g, g, g, g, g, g, g, g, g, g, a, g, a, t, a, t, c, g, c, g, c, a, a, a, t, t, t, c, c, c, t, t, t, a, a, a, t, t, c, c, c, c, c, c, c, t, t, t, g, c, c, g, g, g, t, t, t, g, g, g, a, a, a, c, c, c, t, t, t, c, c, c, t, t, t, g, g, g, a, a, a, t, t, c, a, a, a, c, t, c, c, c, t, a, a, a, g, g, g, a, a, a, t, t, t, a, a, a, c, c, c, a, a, a, g, a, g, c, t, t, c, c, c, c, c, c, g, g, g, t, t, t, c, c, c, c, c, c, t, t, t, t, t, t, c, c, c, c, c, c, a, a, a, a, a, a, g, g, g, g, g, g, c, c, c, c, c, c, a, a, a, g, a, g, g, g, g, t, t, t, c, c, c, a, a, a, c, c, c, c, c, c, a, a, a, t, t, t, c, c, c, t, t, t, c, c, c, a, a, a, g, g, g, c, c, c, c, c, c, g, g, g, a, a, a, c, c, c, a, a, a, a, g, a, g, g, g, t, t, t, c, c, c, c, c, c, a, a, c, t, c, t, c, c, c, a, a, a, g, c, g, c, c, t, a, a, a, c, c, c, c, c, c, g, g, g, c, c, c, c, c, c, t, t, t, a, a, a, c, c, c, c, c, t, t, t, t, g, g, g, c, c, c, a, a, a, g, g, g, t, t, t, g, g, g, g, g, g, a, a, a, g, g, a, c, c, c, a, a, a, g, g, g, c, t, c, c, c, c, t, t, t, g, g, g, a, a, c, a, a, a, g, g, g, g, g, g, c, c, c, c, c, c, t, t, t, c, c, c, g, g, g, g, g, g, a, a, a, c, c, c, a, a, a, c, c, c, c, c, c, g, g, g, c, c, c, c, c, c, a, a, a, t, t, t, g, a, c, t, t, t, a, a, a, t, t, c, t, t, t, a, a, a, c, c, c, n, t, t, n, g, g, n, t, t, n, a, g, n, c, c, n, g, g, n, a, a, n, g, g, n, a, a, n, c, c, n, a, a, n, a, a, n, c, c, n, a, a, n, c, c, n, c, c, n, c, c, n, t, t, n, t, t, n, t, t, n, a, a, n, g, g, n, a, a, n, t, t, n, a, a, n, g, g, n, t, t, n, c, c, n, g, g, n, t, t, n, g, g, n, t, t, n, c, c, n, t, t, n, g, g, n, g, g, n, t, t, n, a, a, n, c, c, n, a, a, n, c, c, n, t, t, n, t, t, n, g, g, n, g, g, g, g, g, g, g, g, c, c, c, c, c, c, a, a, a, a, g, g, g, g, g, g, g, g, a, a, a, a, g, a, c, c, c, c, c, c, c, c, c, t, t, t, g, g, g, g, g, g, t, t, t, c, c, c, a, a, a, c, c, c, c, c, c, g, g, g, t, t, t, c, c, c, t, t, t, c, c, c, c, c, c, t, t, t, c, c, c, a, a, a, g, g, g
#> Sequences
#> 1 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATGTCCATCACAGTGGGAGCACCAATTACAATCCCTCCCTCAAGCGTCGAGTCACCATGTCAGTAGACACGGCCAGGAAGCAGTTGTCCCTGAAATTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTCTGTGCGAGAGGCGCCGGGGACTACAGCACTCCCTTTGACTACTGGGGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGATATATTCATTACAGTGGGAACTCCTTCTACAACCCCTCCCTCAAAAGTCGAGTCACCATGTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAGGTTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTCTGTGCGAGAGGCGCCGGGGACTACGCCACTCCCTTTGACTACTGGGGCCCGGGAACCCTGGTCACCGTCTCCTCAG, 42, 643, 26, 301, IGHV4-61*01, IGHV4-61*01, IGHJ4*01, IGHJ4*01, ggtggctccgtcagcagtggtggttactac, ggtggctccgtcagcagtggtggttactac, GTCCATCACAGTGGGAGCACC, ATTCATTACAGTGGGAACTCC, TGTGCGAGAGGCGCCGGGGACTACAGCACTCCCTTTGACTACTGG, TGTGCGAGAGGCGCCGGGGACTACGCCACTCCCTTTGACTACTGG, caggtgcagctgcaggagtcgggcccaggactggtgaagccttcggagaccctgtccctcacctgcactgtctct, caggtgcagctgcaggagtcgggcccaggactggtgaagccttcggagaccctgtccctcacctgcactgtctct, tggagctggatccggcagCCCCCAGGGAAGGGACTGGAGTGGATTGGGTAT, tggagctggatccggcagCCCCCAGGGAAGGGACTGGAGTGGATTGGATAT, AATTACAATCCCTCCCTCAAGCGTCGAGTCACCATGTCAGTAGACACGGCCAGGAAGCAGTTGTCCCTGAAATTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTC, TTCTACAACCCCTCCCTCAAAAGTCGAGTCACCATGTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAGGTTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTC, GGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, GGCCCGGGAACCCTGGTCACCGTCTCCTCAG, QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGGYYWSWIRQPPGKGLEWIGYVHHSGSTNYNPSLKRRVTMSVDTARKQLSLKLTSVTAADTAVYF, QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGGYYWSWIRQPPGKGLEWIGYIHYSGNSFYNPSLKSRVTMSVDTSKNQFSLRLTSVTAADTAVYF, GQGALV~SPSPQ, GPGTLV~SPSPQ
#> 2 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGTACCAACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCATTAGACACGTCCAAGAACCAGTTCTCCCTGAACCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTTTTGTGCGAGAGATCATCACAGTTTCTATGATACTAGTGGTTATTATCCCTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGAATATCTATTACAGTGGGACTACCAACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCCTTAGACACGTCCAAGAACCAGTTCTCCCTGACCCTGAGGTCTGTGACCGCTGCGGACACGGCCGTGTATTTTTGTGCGAGAGATCATCACAGTTTCTATGATACAAGTGGTTATTATCCCTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, 119, 123, 290, 53, IGHV4-61*01, IGHV4-61*01, IGHJ4*01, IGHJ4*01, ggtggctccgtcagcagtggtggttactac, ggtggctccgtcagcagtggtggttactac, ATCTATTACAGTGGGAGTACC, ATCTATTACAGTGGGACTACC, TGTGCGAGAGATCATCACAGTTTCTATGATACTAGTGGTTATTATCCCTACTTTGACTACTGG, TGTGCGAGAGATCATCACAGTTTCTATGATACAAGTGGTTATTATCCCTACTTTGACTACTGG, caggtgcagctgcaggagtcgggcccaggactggtgaagccttcggagaccctgtccctcacctgcactgtctct, caggtgcagctgcaggagtcgggcccaggactggtgaagccttcggagaccctgtccctcacctgcactgtctct, tggagctggatccggcagcccccagggaagggactgGAGTGGATTGGGTAT, tggagctggatccggcagcccccagggaagggactgGAGTGGATTGGGAAT, AACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCATTAGACACGTCCAAGAACCAGTTCTCCCTGAACCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTTT, AACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCCTTAGACACGTCCAAGAACCAGTTCTCCCTGACCCTGAGGTCTGTGACCGCTGCGGACACGGCCGTGTATTTT, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGGYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVSISLDTSKNQFSLNLSSVTAADTAVYF, QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGGYYWSWIRQPPGKGLEWIGNIYYSGTTNYNPSLKSRVSISLDTSKNQFSLTLRSVTAADTAVYF, GQGTLV~SPSPQ, GQGTLV~SPSPQ
#> 3 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGACCAGGTCACCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGTGAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAAGCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGAATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGACCAGGTCAGCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGTAAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAACCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, 416, 792, 21, 777, IGHV5-51*01, IGHV5-51*01, IGHJ4*01, IGHJ4*01, ggatacagctttaccagctactgg, ggatacagctttaccagctactgg, ATCTATCCTGGTGACTCTGATACC, ATCTATCCTGGTGACTCTGATACC, TGTGTGAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAAGCTTTGACTACTGG, TGTGTAAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAACCTTTGACTACTGG, gaggtgcagctggtgcagtctggagcagaggtgaaaaagcccggggagtctctgaagatctcctgtaagggttct, gaggtgcagctggtgcagtctggagcagaggtgaaaaagcccggggagtctctgaagatctcctgtaagggttct, atcggctgggtgcgccagatgcccgggaaaggcctgGAGTGGATGGGGATC, atcggctgggtgcgccagatgcccgggaaaggcctgGAGTGGATGGGAATC, AGATACAGCCCGTCCTTCCAAGACCAGGTCACCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTAC, AGATACAGCCCGTCCTTCCAAGACCAGGTCAGCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTAC, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQDQVTMSVGKSIGTAYLQWSSLKASDTAMYY, EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQDQVSMSVGKSIGTAYLQWSSLKASDTAMYY, GQGTLV~SPSPQ, GQGTLV~SPSPQ
#> 4 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGAAAAGGCCTGGAGTGGGTGGGATCGATCTATCCTCGTGACTCTGATATCAGATACAATCCGTCCTTCCAAGGCCAAGTCACCATCTCAGCCGACAGGTCCACCACCACCGCCTACCTGCAGTGGAGCAGTCTGAAGGCCTCGGACACCGCCATATATTACTGTACGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGGGGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGTTGGGGAGCATCTACCCTCGTGACTCTGACACTAGATACAGTCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCCTCAGTACCGCCTACTTGCAGTGGAACAGCCTGCAGGCCTCGGACACCGCCATCTACTACTGTGCGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, 283, 987, 184, 57, IGHV5-51*01, IGHV5-51*01, IGHJ5*01, IGHJ5*01, ggatacagctttaccagctactgg, ggatacagctttaccagctactgg, ATCTATCCTCGTGACTCTGATATC, ATCTACCCTCGTGACTCTGACACT, TGTACGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGG, TGTGCGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGG, gaggtgcagctggtgcagtctggagcagaggtgaaaaagcccggggagtctctgaagatctcctgtaagggttct, gaggtgcagctggtgcagtctggagcagaggtgaaaaagcccggggagtctctgaagatctcctgtaagggttct, atcggctgggtgcgccagatgCCCGGAAAAGGCCTGGAGTGGGTGGGATCG, atcggctgggtgcgccagatgCCCGGGAAAGGCCTGGAGTGGTTGGGGAGC, AGATACAATCCGTCCTTCCAAGGCCAAGTCACCATCTCAGCCGACAGGTCCACCACCACCGCCTACCTGCAGTGGAGCAGTCTGAAGGCCTCGGACACCGCCATATATTAC, AGATACAGTCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCCTCAGTACCGCCTACTTGCAGTGGAACAGCCTGCAGGCCTCGGACACCGCCATCTACTAC, GGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWVGSIYPRDSDIRYNPSFQGQVTISADRSTTTAYLQWSSLKASDTAIYY, EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWLGSIYPRDSDTRYSPSFQGQVTISADKSLSTAYLQWNSLQASDTAIYY, GQGALV~SPSPQ, GQGTLV~SPSPQ
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