ArticleNucleic acids research2018
CSAR-web: a web server of contig scaffolding using algebraic rearrangements.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Whole-genome analysis and enzymatic profiling of Bacillus spizizenii as a xylanase-producing source from Iran.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Genomic and enzymatic insights into α-amylase-producing Bacillus spizizenii strains isolated from Isfahan province, Iran.PloS one · 2025Article
- Serovar-specific genomic features ofFrontiers in molecular biosciences · 2025Article
- Draft genome sequence ofMicrobiology resource announcements · 2024Article
- Yersinia entomophaga Tc toxin is released by T10SS-dependent lysis of specialized cell subpopulations.Nature microbiology · 2024Article
- Biotechnological Key Genes of theMicroorganisms · 2023Article
- Genomic Insights into the Microbial AgentMicroorganisms · 2023Article
- Characterization of a NovelMicroorganisms · 2023Article
- Functional annotation and comparative analysis of fourSaudi journal of biological sciences · 2023Article
- Characterization of NRPS and PKS genes involved in the biosynthesis of SMs in Alternaria dauci including the phytotoxic polyketide aldaulactone.Scientific reports · 2022Article
- Temperate Bacteriophages (Prophages) inFrontiers in microbiology · 2020Article
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Authors and funding
2 authors.
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Abstract
CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism. It takes as input a target genome in multi-FASTA format and a reference genome in FASTA or multi-FASTA format, depending on whether the reference genome is complete or incomplete, respectively. In addition, it requires the users to choose either 'NUCmer on nucleotides' or 'PROmer on translated amino acids' for CSAR-web to identify conserved genomic markers (i.e. matched sequence regions) between the target and reference genomes, which are used by the rearrangement-based scaffolding algorithm in CSAR-web to order and orient the contigs of the target genome based on the reference genome. In the output page, CSAR-web displays its scaffolding result in a graphical mode (i.e. scalable dotplot) allowing the users to visually validate the correctness of scaffolded contigs and in a tabular mode allowing the users to view the details of scaffolds. CSAR-web is available online at http://genome.cs.nthu.edu.tw/CSAR-web.
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Registered trials
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