ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Indexing labeled sequences | JoVE Visualize

Home
Research Domains
Information And Computing Sciences

Indexing labeled sequences

Tatiana Rocher¹, Mathieu Giraud¹, Mikaël Salson¹

¹Université de Lille, CNRS, Centrale Lille, Inria, UMR 9189 CRIStAL, Lille, France.

Peerj. Computer Science|April 5, 2021

Related Experiment Videos

View abstract on PubMed

Summary

New indexes efficiently store and query labeled DNA sequences, improving insights into lymphocyte repertoires for immunology and onco-hematology research. These methods enhance analysis of V(D)J recombination data.

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Text labeling annotates sequences with functional information, like genes on DNA.
V(D)J recombination in lymphocytes involves short gene sequences crucial for immune repertoire studies.
Sequencing these regions yields labeled sequences valuable for onco-hematology and immunology.

Purpose of the Study:

To develop and evaluate novel indexing methods for labeled text data.
To improve the efficiency of querying and analyzing sequences with associated labels.

Main Methods:

Introduced two indexes: TL-index and TL<sub>BW</sub>-index, utilizing Burrows-Wheeler Transform and Wavelet Trees.
Indexes store text and compressed label sequences, requiring space proportional to data entropy.
Implemented indexes in C++ for performance comparison.

Main Results:

Indexes enable efficient counting and locating of labeled patterns within texts.
TL<sub>BW</sub>-index shows superior performance for combined pattern-label queries.
Performance was validated on both synthetic and real V(D)J recombination sequence data.

Conclusions:

The proposed indexes offer significant improvements for indexing and querying labeled texts.
These advancements facilitate deeper analysis of lymphocyte repertoires in hematological and immunological research.

Keywords:

Burrows–Wheeler transform

Related Concept Videos

Library And Information Studies

Indexing Labeled Sequences

Data structures

V(D)J recombination

Related Experiment Videos