AutomAted RepeaT Identifier (AARTI): A tool to identify common, polymorphic, and unique microsatellites

Kumar, Sumit; Singh, Ashutosh; Kumar, Nitish; Choudhary, Mamta; Choudhary, B.K.; Shanker, Asheesh

doi:10.1016/j.mito.2022.06.002

Cited by 2 publications

(1 citation statement)

References 26 publications

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“…The utility of these tools is primarily determined by their ability to identify complex SSR structures, their flexibility, their ease of maintenance, and the minimal computer skills required for proper use. These tools include TRF (Benson, 1999), TROLL (Castelo et al, 2002), mreps (Kolpakov et al, 2003), SciRoko (Kofler et al, 2007), MsDetector (Girgis and Sheetlin, 2013), GMATo (Wang et al, 2013), GMATA (Wang and Wang, 2016), MISA (Thiel et al, 2003), PolyMorphPredict (Das et al, 2019), ESAP Plus (Ponyared et al, 2016, SAT (Dereeper et al, 2007), AARTI (Kumar et al, 2022), ESMP (Sarmah et al, 2012), WebSat (Martins et al, 2009), SSRPrimer (Jewell et al, 2006), WGSSAT (Pandey et al, 2018), and IMEx (Mudunuri and Nagarajaram, 2007). Among these tools, MISA is a widely used tool for SSR detection due to its early development, efficiency, and simplicity.…”

Section: Introductionmentioning

confidence: 99%

MegaSSR: a web server for large scale microsatellite identification, classification, and marker development

Mokhtar,

Alsamman,

El Allali

2023

Front. Plant Sci.

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Next-generation sequencing technologies have opened new avenues for using genomic data to study and develop molecular markers and improve genetic resources. Simple Sequence Repeats (SSRs) as genetic markers are increasingly used in molecular diversity and molecular breeding programs that require bioinformatics pipelines to analyze the large amounts of data. Therefore, there is an ongoing need for online tools that provide computational resources with minimal effort and maximum efficiency, including automated development of SSR markers. These tools should be flexible, customizable, and able to handle the ever-increasing amount of genomic data. Here we introduce MegaSSR (https://bioinformatics.um6p.ma/MegaSSR), a web server and a standalone pipeline that enables the design of SSR markers in any target genome. MegaSSR allows users to design targeted PCR-based primers for their selected SSR repeats and includes multiple tools that initiate computational pipelines for SSR mining, classification, comparisons, PCR primer design, in silico PCR validation, and statistical visualization. MegaSSR results can be accessed, searched, downloaded, and visualized with user-friendly web-based tools. These tools provide graphs and tables showing various aspects of SSR markers and corresponding PCR primers. MegaSSR will accelerate ongoing research in plant species and assist breeding programs in their efforts to improve current genomic resources.

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Section: Introductionmentioning

confidence: 99%

MegaSSR: a web server for large scale microsatellite identification, classification, and marker development

Mokhtar,

Alsamman,

El Allali

2023

Front. Plant Sci.

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Scan-Find-Scan-Model: Discrete Site-Targeted Suppressor Design Strategy for Amyloid-β

Bhagavatula¹,

Sarkar

Santra

et al. 2022

ACS Chem. Neurosci.

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Alzheimer’s disease is undoubtedly the most well-studied neurodegenerative disease. Consequently, the amyloid-β (Aβ) protein ranks at the top in terms of getting attention from the scientific community for structural property-based characterization. Even after decades of extensive research, there is existing volatility in terms of understanding and hence the effective tackling procedures against the disease that arises due to the lack of knowledge of both specific target- and site-specific drugs. Here, we develop a multidimensional approach based on the characterization of the common static-dynamic-thermodynamic trait of the monomeric protein, which efficiently identifies a small target sequence that contains an inherent tendency to misfold and consequently aggregate. The robustness of the identification of the target sequence comes with an abundance of a priori knowledge about the length and sequence of the target and hence guides toward effective designing of the target-specific drug with a very low probability of bottleneck and failure. Based on the target sequence information, we further identified a specific mutant that showed the maximum potential to act as a destabilizer of the monomeric protein as well as enormous success as an aggregation suppressor. We eventually tested the drug efficacy by estimating the extent of modulation of binding affinity existing within the fibrillar form of the Aβ protein due to a single-point mutation and hence provided a proof of concept of the entire protocol.

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AutomAted RepeaT Identifier (AARTI): A tool to identify common, polymorphic, and unique microsatellites

Cited by 2 publications

References 26 publications

MegaSSR: a web server for large scale microsatellite identification, classification, and marker development

MegaSSR: a web server for large scale microsatellite identification, classification, and marker development

Scan-Find-Scan-Model: Discrete Site-Targeted Suppressor Design Strategy for Amyloid-β

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