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SMART is a web-based tool that allows users to search for domains in proteins and annotate their functions and structures. It uses HMMs, BLAST, and other methods to detect and classify domains, and provides links to Entrez and other databases for further information.
Mar 6, 2009 · SMART is an online tool for the identification and annotation of protein domains. It provides a user-friendly platform for the exploration and comparative study of domain architectures in both proteins and genes. The current release of SMART contains manually curated models for 784 protein domains.
Dec 27, 2023 · Bioinformatics tools are essential for understanding and unraveling the complexities of biological data. From organizing information to predicting protein structures and conducting genomic analysis, these tools benefit researchers, scientists, and students alike.
SMART, a simple modular architecture research tool: identification of signaling domains. [PMID: 9600884] Schultz J, Milpetz F, Bork P, Ponting CP. Abstract. Proc Natl Acad Sci U S A. 1998:95 (11) | 2260 Citations (from Europe PMC, 2024-06-22) Showing 1 to 5 of 5 entries.
- Simple Modular Architecture Research Tool
- 1998
- 2017
- Home
- Differential Cpgs
- Methylation Diy
- Correlation
- Survival
The home page first displays the number of DNA methylation samples available from TCGA project, colored by sample types (i.e., Normal and Tumor), for users to gain an overview of the sample size of the cancer type of interest. Next, the SMART App provides a quick search interface. Users can enter a gene symbol (e.g., ERBB2) into the ‘Quick start’ b...
Differential analysis is a common approach in cancer research by comparing tumor samples vs. normal samples for identifying aberrantly methylated CpGs. Meanwhile, clustering of the CpGs with similar methylation patterns along the chromosomes may reflect the genomic mechanisms leading to specific methylation characteristics . Therefore, the SMART Ap...
This module provides functions for users to comprehensively analyze DNA methylation taking other omics data and clinical stages into consideration. The first panel generates custom box plots for users for compare CpGs of genes between normal and tumor samples in a given cancer type. Users can select multiple probes at the same time for easy visibil...
DNA methylation is often correlated with gene expression. The correlation function of SMART App performs correlation analysis between gene expression and methylation for any given sets of TCGA, using methods including Pearson, Spearman, and Kendall correlation statistics. The UCSC Xena provides the re-computed expression data of TCGA for 198,619 tr...
The SMART App performs overall survival (OS) and disease-free internal (DFI)-related survival analysis based on methylation levels. This function allows users to select their custom cancer types for overall or disease-free survival analysis. Cox regression analysis is a popular method for evaluating the prognostic value of individual variables. To ...
- Yin Li, Di Ge, Chunlai Lu
- 2019
Nov 29, 2023 · Streamline genomic data analysis with the leading bioinformatics platforms. Our guide compares features across 5 top tools – UGENE, SAMTools, GenomeSpace, MEGA, and IGV. Access power user tips.
The list of bioinformatics software tools can be split up according to the license used: List of proprietary bioinformatics software. List of open-source bioinformatics software. Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: Sequence analysis software.
