MegaSSR: a web server for large scale microsatellite identification, classification, and marker development
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 bio...
| Main Authors: | , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Frontiers Media
2023
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/162573 |
| _version_ | 1855540968065859584 |
|---|---|
| author | Mokhtar, Morad M. Alsamman, Alsamman M. El Allali, Achraf |
| author_browse | Alsamman, Alsamman M. El Allali, Achraf Mokhtar, Morad M. |
| author_facet | Mokhtar, Morad M. Alsamman, Alsamman M. El Allali, Achraf |
| author_sort | Mokhtar, Morad M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace162573 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1625732026-01-15T02:19:22Z MegaSSR: a web server for large scale microsatellite identification, classification, and marker development Mokhtar, Morad M. Alsamman, Alsamman M. El Allali, Achraf simple sequence repeats ssr markers megassr web server non-redundant ssr library bioinformatic pipeline. 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. 2023-12-14 2024-11-21T21:38:51Z 2024-11-21T21:38:51Z Journal Article https://hdl.handle.net/10568/162573 en Open Access application/pdf Frontiers Media Morad M. Mokhtar, Alsamman M. Alsamman, Achraf El Allali. (14/12/2023). MegaSSR: a web server for large scale microsatellite identification, classification, and marker development. Frontiers in Plant Science, 14. |
| spellingShingle | simple sequence repeats ssr markers megassr web server non-redundant ssr library bioinformatic pipeline. Mokhtar, Morad M. Alsamman, Alsamman M. El Allali, Achraf MegaSSR: a web server for large scale microsatellite identification, classification, and marker development |
| title | MegaSSR: a web server for large scale microsatellite identification, classification, and marker development |
| title_full | MegaSSR: a web server for large scale microsatellite identification, classification, and marker development |
| title_fullStr | MegaSSR: a web server for large scale microsatellite identification, classification, and marker development |
| title_full_unstemmed | MegaSSR: a web server for large scale microsatellite identification, classification, and marker development |
| title_short | MegaSSR: a web server for large scale microsatellite identification, classification, and marker development |
| title_sort | megassr a web server for large scale microsatellite identification classification and marker development |
| topic | simple sequence repeats ssr markers megassr web server non-redundant ssr library bioinformatic pipeline. |
| url | https://hdl.handle.net/10568/162573 |
| work_keys_str_mv | AT mokhtarmoradm megassrawebserverforlargescalemicrosatelliteidentificationclassificationandmarkerdevelopment AT alsammanalsammanm megassrawebserverforlargescalemicrosatelliteidentificationclassificationandmarkerdevelopment AT elallaliachraf megassrawebserverforlargescalemicrosatelliteidentificationclassificationandmarkerdevelopment |