Indexing labeled sequences

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...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:PeerJ. Computer science Jg. 4; S. e148 - 14
Hauptverfasser: Rocher, Tatiana, Giraud, Mathieu, Salson, Mikaël
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States PeerJ. Ltd 26.03.2018
PeerJ, Inc
PeerJ
PeerJ Inc
Schlagworte:
Algorithms and Analysis of Algorithms
Analysis
Annotations
Bioinformatics
Burrows-Wheeler transform
Computational Biology
Computational Complexity
Computer Science
Data compression
Data structures
Data Structures and Algorithms
Deoxyribonucleic acid
DNA
DNA sequencing
Entropy
Gene sequencing
Genes
Hematology
Immunology
Indexing (Content analysis)
Labels
Leaves
Leukemia
Lymphocytes
Methods
Queries
Text indexing
Texts
V(D)J recombination
Wavelet analysis
Wavelet Tree
France
Text indexing
Data structures
Burrows–Wheeler transform
Wavelet Tree
V(D)J recombination
ISSN:2376-5992, 2376-5992
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung: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. 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 -index). Both indexes need a space related to the entropy of the labeled text. These indexes allow efficient text-label queries to count and find labeled patterns. The TL -index has an overhead on simple label queries but is very efficient on combined pattern-label queries. We implemented the indexes in C++ and compared them against a baseline solution on pseudo-random as well as on V(D)J labeled texts. New indexes such as the ones we proposed improve the way we index and query labeled texts as, for instance, lymphocyte repertoire for hematological and immunological studies.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ISSN:2376-5992
2376-5992
DOI:10.7717/peerj-cs.148