Fast Exact String to D-Texts Alignments

Njagi Mwaniki; Erik Garrison; Nadia Pisanti

Research.Publish.Connect.

*Please fill out at least one Field. *Value must be an number!

Title:
ISBN:
Year:
Acronym:
Subject:

Advanced Search Proceedings Search

If you're looking for an exact phrase use quotation marks on text fields.

*Please fill out at least one Field.

Title:
Author:
Affiliation:
Subject:

Advanced Search Papers Search

If you're looking for an exact phrase use quotation marks on text fields.

*Please fill out at least one Field.

Name:
Affiliation:
Country:
Conference:
Subject:

Advanced Search Authors Search

If you're looking for an exact phrase use quotation marks on text fields.

*Please fill out at least one Field.

Name:
Country:
Subject:

Advanced Search Affiliations Search

If you're looking for an exact phrase use quotation marks on text fields.

Proceedings

Proceedings Search *Please fill out at least one Field. *Value must be an number!

Title:
ISBN:
Year:
Acronym:
Subject:

Advanced Search Proceedings Search

If you're looking for an exact phrase use quotation marks on text fields.

Papers

Papers Search *Please fill out at least one Field.

Title:
Author:
Affiliation:
Subject:

Advanced Search Papers Search

If you're looking for an exact phrase use quotation marks on text fields.

Authors

Authors Search *Please fill out at least one Field.

Name:
Affiliation:
Country:
Conference:
Subject:

Advanced Search Authors Search

If you're looking for an exact phrase use quotation marks on text fields.

Advanced Search

Paper

Fast Exact String to D-Texts Alignments

Topics: Sequence Analysis

In Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOSTEC, 70-79, 2023 , Lisbon, Portugal

Authors: Njagi Mwaniki ¹ ; Erik Garrison ² and Nadia Pisanti ¹

Affiliations: ¹ University of Pisa, Italy ; ² University of Tennessee Health Science Center, U.S.A.

Keyword(s): D-string, Pangenome, Pattern Matching.

Abstract: A D-strings is a degenerate string representing similar and aligned strings by collapsing common fragments and highlighting variants. D-strings can represent a MSA or a pan-genome. In this paper we propose a new, fast and exact method to align a string to a D-string. In recent years, aligning a sequence to a pangenome has become a central problem in computational genomics and pangenomics. A fast and accurate solution to this problem can serve as a toolkit to many crucial tasks such as read-correction, Multiple Sequences Alignment (MSA), genome assemblies, and variant calling, just to name a few. An implementation of our tool is publicly available on github at https://github.com/urbanslug/dsa.

CC BY-NC-ND 4.0

Guest: Register as new SciTePress user now for free.

SciTePress user: please login.

My Papers

You are not signed in, therefore limits apply to your IP address 3.144.255.116

In the current month:

Recent papers: 100 available of 100 total

2⁺ years older papers: 200 available of 200 total

Paper citation in several formats:

Mwaniki, N.; Garrison, E. and Pisanti, N. (2023). Fast Exact String to D-Texts Alignments. In Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2023) - BIOINFORMATICS; ISBN 978-989-758-631-6; ISSN 2184-4305, SciTePress, pages 70-79. DOI: 10.5220/0011666900003414

@conference{bioinformatics23,
author={Njagi Mwaniki. and Erik Garrison. and Nadia Pisanti.},
title={Fast Exact String to D-Texts Alignments},
booktitle={Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2023) - BIOINFORMATICS},
year={2023},
pages={70-79},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0011666900003414},
isbn={978-989-758-631-6},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2023) - BIOINFORMATICS
TI - Fast Exact String to D-Texts Alignments
SN - 978-989-758-631-6
IS - 2184-4305
AU - Mwaniki, N.
AU - Garrison, E.
AU - Pisanti, N.
PY - 2023
SP - 70
EP - 79
DO - 10.5220/0011666900003414
PB - SciTePress