Indexing labeled sequences.

ABSTRACT:

Background

Labels are a way to add some information on a text, such as functional annotations such as genes on a DNA sequences. V(D)J recombinations are DNA recombinations involving two or three short genes in lymphocytes. Sequencing this short region (500 bp or less) produces labeled sequences and brings insight in the lymphocyte repertoire for onco-hematology or immunology studies.

Methods

We present two indexes for a text with non-overlapping labels. They store the text in a Burrows-Wheeler transform (BWT) and a compressed label sequence in a Wavelet Tree. The label sequence is taken in the order of the text (TL-index) or in the order of the BWT (TL_BW-index). Both indexes need a space related to the entropy of the labeled text.

Results

These index

SUBMITTER: Rocher T 

PROVIDER: S-EPMC7924554 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature