OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs.

ABSTRACT:

Motivation

High-throughput sequencing of large immune repertoires has enabled the development of methods to predict the probability of generation by V(D)J recombination of T- and B-cell receptors of any specific nucleotide sequence. These generation probabilities are very non-homogeneous, ranging over 20 orders of magnitude in real repertoires. Since the function of a receptor really depends on its protein sequence, it is important to be able to predict this probability of generation at the amino acid level. However, brute-force summation over all the nucleotide sequences with the correct amino acid translation is computationally intractable. The purpose of this paper is to present a solution to this problem.

Results

We use dynamic programming to construct an efficient and f

SUBMITTER: Sethna Z 

PROVIDER: S-EPMC6735909 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature