ArticleNucleic acids research2019
SSRome: an integrated database and pipelines for exploring microsatellites in all organisms.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Pytrf: a python package for finding tandem repeats from genomic sequences.BMC bioinformatics · 2025Article
- Microsatellites explorer: A database of short tandem repeats across genomes.Computational and structural biotechnology journal · 2024Article
- Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb.Database : the journal of biological databases and curation · 2024Article
- pSATdb 2.0: a database of organellar common, polymorphic, and unique microsatellites.Functional & integrative genomics · 2024Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD.The plant genome · 2024Article
- Heterozygosity analysis of spontaneous 2n female gametes and centromere mapping of the diploid Hevea brasiliensis based on full-sib triploid populations.Plant reproduction · 2024Article
- What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools.Frontiers in genetics · 2024Review
- MegaSSR: a web server for large scale microsatellite identification, classification, and marker development.Frontiers in plant science · 2023Article
- PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons.Frontiers in plant science · 2023Article
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- pSATdb: a database of mitochondrial common, polymorphic, and unique microsatellites.Life science alliance · 2022Article
- PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes.Scientific reports · 2021Article
- Developing a new genic SSR primer database in faba bean (Vicia faba L.).Journal of applied genetics · 2021Article
- Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species.Journal of fungi (Basel, Switzerland) · 2021Article
- Generation of Chloroplast Molecular Markers to DifferentiatePlants (Basel, Switzerland) · 2021Article
- BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data.Frontiers in big data · 2021Article
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- Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists.Scientific reports · 2020Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Over the past decade, many databases focusing on microsatellite mining on a genomic scale were released online with at least one of the following major deficiencies: (i) lacking the classification of microsatellites as genic or non-genic, (ii) not comparing microsatellite motifs at both genic and non-genic levels in order to identify unique motifs for each class or (iii) missing SSR marker development. In this study, we have developed 'SSRome' as a web-based, user-friendly, comprehensive and dynamic database with pipelines for exploring microsatellites in 6533 organisms. In the SSRome database, 158 million microsatellite motifs are identified across all taxa, in addition to all the mitochondrial and chloroplast genomes and expressed sequence tags available from NCBI. Moreover, 45.1 million microsatellite markers were developed and classified as genic or non-genic. All the stored motif and marker datasets can be downloaded freely. In addition, SSRome provides three user-friendly tools to identify, classify and compare motifs on either a genome- or transcriptome-wide scale. With the implementation of PHP, HTML and JavaScript, users can upload their data for analysis via a user-friendly GUI. SSRome represents a powerful database and mega-tool that will assist researchers in developing and dissecting microsatellite markers on a high-throughput scale.
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