Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics.
Bioinformatics
; 38(22): 5121-5123, 2022 11 15.
Article
em En
| MEDLINE
| ID: mdl-36179084
ABSTRACT
SUMMARY:
Several high-throughput protein-DNA binding methods currently available produce highly reproducible measurements of binding affinity at the level of the k-mer. However, understanding where a k-mer is positioned along a binding site sequence depends on alignment. Here, we present Top-Down Crawl (TDC), an ultra-rapid tool designed for the alignment of k-mer level data in a rank-dependent and position weight matrix (PWM)-independent manner. As the framework only depends on the rank of the input, the method can accept input from many types of experiments (protein binding microarray, SELEX-seq, SMiLE-seq, etc.) without the need for specialized parameterization. Measuring the performance of the alignment using multiple linear regression with 5-fold cross-validation, we find TDC to perform as well as or better than computationally expensive PWM-based methods. AVAILABILITY AND IMPLEMENTATION TDC can be run online at https//topdowncrawl.usc.edu or locally as a python package available through pip at https//pypi.org/project/TopDownCrawl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Base de dados:
MEDLINE
Assunto principal:
Software
Tipo de estudo:
Risk_factors_studies
Idioma:
En
Ano de publicação:
2022
Tipo de documento:
Article