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Fig. 6 | BMC Bioinformatics

Fig. 6

From: TRIP - T cell receptor/immunoglobulin profiler

Fig. 6

Examples of output tables provided by TRIP. a Clonotypes of all datasets. Each clonotype is presented according to the definition chosen by the user followed by its absolute count of reads, its relative frequency and the convergent evolution, i.e. the different nucleotide sequences encoding the amino acid sequence of each clonotype. b Highly Similar Clonotypes. Clonotypes of the same CDR3 length and differences in the amino acid composition in few positions are merged. Each clonotype is presented followed by the newly-calculated absolute count of reads, its relative frequency and a list of the cluster ids merged. c Elements of the clonotype. Each clonotype presented in the first column of Fig. 1a is also a link that provides a table with all relevant immunogenetic data for that particular clonotype. d Shared Clonotypes. When multiple datasets are analyzed simultaneously, some clonotypes may co-occur in more than one datasets. The clonotypes that were present in >= 2 samples are presented in this table followed by the number of reads assigned to each clonotype in every dataset. The last column of the table is about the number of datasets/samples that shared each clonotype. e Grouped Alignment. This output table is provided after the alignment and the grouping of the identical sequences at amino acid level based on the reference sequences and each row represents a unique amino acid sequence. It includes the number of reads that are identical, the IGHV gene and allele used as reference, the cluster id (clonotype) the sequence corresponds to (the reference sequence is characterized with "-") and the positions of the BcR IG molecule. The amino acids that correspond to the germline are replaced with "-", while the differences remain. f Somatic Hypermutations. This output table is computed based on the alignment table (Fig. 6e) and includes: (i) the gene and allele used, (ii) the actual mutation stating the amino acid of the reference sequence and the new one including the position of the change, (iii) the region where the change occurs based on IMGT, (iv) the type of the mutation with regards to the physicochemical properties, (v) the number of sequences carrying the particular change and (vi) the relative frequency of every mutation

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