PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F23%3A00579941" target="_blank" >RIV/61388963:_____/23:00579941 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11320/23:10485049

Result on the web

<a href="https://doi.org/10.1186/s12859-023-05613-5" target="_blank" >https://doi.org/10.1186/s12859-023-05613-5</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s12859-023-05613-5" target="_blank" >10.1186/s12859-023-05613-5</a>

Result language

angličtina

Original language name

PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction

Original language description

Background: The specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the recognition can be influenced not only by the binding motif but by the larger context of the binding site. In this work, we present a novel heuristic algorithm that can reconstruct the unique binding sites captured in a sequencing experiment without using the reference genome. Results: We present PAPerFly, the Partial Assembly-based Peak Finder, a tool for the binding site and binding context reconstruction from the sequencing data without any prior knowledge. This tool operates without the need to know the reference genome of the respective organism. We employ algorithmic approaches that are used during genome assembly. The proposed algorithm constructs a de Bruijn graph from the sequencing data. Based on this graph, sequences and their enrichment are reconstructed using a novel heuristic algorithm. The reconstructed sequences are aligned and the peaks in the sequence enrichment are identified. Our approach was tested by processing several ChIP-seq experiments available in the ENCODE database and comparing the results of Paperfly and standard methods. Conclusions: We show that PAPerFly, an algorithm tailored for experiment analysis without the reference genome, yields better results than an aggregation of ChIP-seq agnostic tools. Our tool is freely available at https://github.com/Caeph/paperfly/ or on Zenodo (https://doi.org/10.5281/zenodo.7116424).

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/EF16_019%2F0000729" target="_blank" >EF16_019/0000729: Chemical biology for drugging undruggable targets</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

BMC Bioinformatics

ISSN

1471-2105

e-ISSN

1471-2105

Volume of the periodical

24

Issue of the periodical within the volume

1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

15

Pages from-to

487

UT code for WoS article

001129413200002

EID of the result in the Scopus database

2-s2.0-85180128666