ginmappeR: an unified approach for integrating gene and protein identifiers across biological sequence databases

被引：1

作者：

Sola, Fernando ^{[1
]}

Ayala, Daniel ^{[1
]}

Pulido, Marina ^{[2
,3
,4
]}

Ayala, Rafael ^{[5
]}

Lopez-Cerero, Lorena ^{[2
,3
,4
]}

Hernandez, Inma ^{[1
]}

Ruiz, David ^{[1
]}

机构：

[1] Univ Seville, SCORE Lab, DEAL, ETSII, Reina Mercedes Ave S-N, Seville 41012, Spain

[2] Univ Seville, Dept Microbiol, Seville 41009, Spain

[3] Univ Seville, Virgen Macarena Univ Hosp, Inst Biomed Seville, CSIC, Seville 41013, Spain

[4] Ctr Invest Biomed Red Enfermedades Infecciosas CI, Madrid 28029, Spain

[5] Technol Grad Univ, Okinawa Inst Sci, Mol Cryo Electron Microscopy Unit, Onnason, Okinawa 9040411, Japan

来源：

BIOINFORMATICS ADVANCES | 2024年 / 4卷 / 01期

关键词：

D O I：

10.1093/bioadv/vbae129

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The proliferation of biological sequence data, due to developments in molecular biology techniques, has led to the creation of numerous open access databases on gene and protein sequencing. However, the lack of direct equivalence between identifiers across these databases difficults data integration. To address this challenge, we introduce ginmappeR, an integrated R package facilitating the translation of gene and protein identifiers between databases. By providing a unified interface, ginmappeR streamlines the integration of diverse data sources into biological workflows, so it enhances efficiency and user experience.Availability and implementation from Bioconductor: https://bioconductor.org/packages/ginmappeR

引用

页数：5

共 43 条

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[35] An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom
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Paradzik, Tina
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[36] PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships
Pan, Tong
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Wang, Zhikang
Gasser, Robin B.
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[37] Isolation of a cDNA for a novel human RING finger protein gene, RNF18, by the virtual transcribed sequence (VTS) approach
Yoshikawa, T
Seki, N
Azuma, T
Masuho, Y
Muramatsu, M
Miyajima, N
Saito, T
BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION, 2000, 1493 (03): : 349 - 355
[38] Statistical Testing for Protein Equivalence Identifies Core Functional Modules Conserved across 360 Cancer Cell Lines and Presents a General Approach to Investigating Biological Systems
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Myung, Junia J. K.
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[39] Analysis of the gene expressed in Clonorchis sinensis adults using the expressed sequence tag approach and construction of a DNA vaccine encoding fatty acid binding protein
Lee, JS
Lee, J
Park, SJ
Yong, TS
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[40] COMPREHENSIVE 2-DIMENSIONAL GEL PROTEIN DATABASES OFFER A GLOBAL APPROACH TO THE ANALYSIS OF HUMAN-CELLS - THE TRANSFORMED AMNION CELLS (AMA) MASTER DATABASE AND ITS LINK TO GENOME DNA-SEQUENCE DATA
CELIS, JE
GESSER, B
RASMUSSEN, HH
MADSEN, P
LEFFERS, H
DEJGAARD, K
HONORE, B
OLSEN, E
RATZ, G
LAURIDSEN, JB
BASSE, B
MOURITZEN, S
HELLERUP, M
ANDERSEN, A
WALBUM, E
CELIS, A
BAUW, G
PUYPE, M
VANDAMME, J
VANDEKERCKHOVE, J
ELECTROPHORESIS, 1990, 11 (12) : 989 - 1071

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