Searches for germline variable (V), diversity (D) and joining (J) genes matches for T-cell receptor (TCR) and immunoglobulin (IG) sequences using BLAST algorithm. Works both with amino-acid and nucleotide sequences and supports alignment to IMGT(R) germline sequence database, as well as custom databases. Provides information of CDR1,2 and FR1,2,3 region markup and germline sequence mutations.
Provides immunology researchers with powerful data analysis infrastructure. VDJserver offers tools for performing immune repertoire analysis with a focus on collaboration, streamlined metadata capture, and reproducibility. It also allow to get basic repertoire characterization results for both B cell receptor and T cell receptor repertoires.
Identifies variable (V) and joining (J) segments, as well as CDR3 region sequences using K-string-based algorithm for translated nucleotide queries. Specifically designed to handle short reads, the tool correctly accounts for sequencing reads with missing CDR3 region in order to provide an unbiased V/J segment usage data.
A software package to identify and analyze antigen receptors from high-throughput sequence libraries. ClonotypeR is designed to process, organize and analyze very large numbers of sequences, in the order of millions, typically produced by Roche 454 or Illumina instruments, and is made of two parts. The first contains shell scripts and reference segment sequences to produce a data file where each line represents the detection of a clonotype in a sequence read. The second part is a R module available from Bioconductor, to load and filter the data, and prepare clonotype abundance tables ready for analysis with third-party tools for differential representation analysis, sample clustering, etc.
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