WindowMasker: window-based masker for sequenced genomes

By Aleksandr Morgulis, E. Gertz, Alejandro A. Schäffer, Richa Agarwala. Bioinform., 2006

295 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/694aba3fd0372987713e747374797455f052725d

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In Molecular Biology

1. David Haussler
2. W. James Kent
3. Robert M. Kuhn
4. Thomas L. Madden
5. Mark Diekhans
6. Kate R. Rosenbloom
7. Donna Karolchik
8. George F. Coulouris

Citations in the corpus

• Adaptive seeds tame genomic sequence comparison. (2011, unknown): “WindowMasker (Morgulis et al. 2006) was used for masking repeats.”
• Database indexing for production MegaBLAST searches (2008, methodology): “The indices were created from unmasked databases and databases masked with WindowMasker (Morgulis et al. , 2006a), including low-complexity filtering by DUST (Morgulis et al. , 2006b).”
• A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences (2006, unknown): “It is also used in Windowmasker, our new tool for masking repetitive and low-complexity sequences (Morgulis et al. , 2006).”
• Significantly improving the quality of genome assemblies through curation (2020, unknown): “RefSeq mitochondria [25] and plastid [26] assemblies other species megaBLAST e-value <= 1e-4, match score >= 100, sequence identity >= 98%; ignore regions also matching highly conserved rDNAs Windowmasked [27] RefSeq genomes [28]”
• BLAST+: architecture and applications (2009, methodology): “A specialized tool, such as WindowMasker [19] or RepeatMasker [10], can provide masking information for a single-species database when it is created, and it becomes unnecessary to mask every query.”
• Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing (2021, unknown): “0, -mk_counts -sformat obinary genome_size 882654037) [31].”
• Personalized Copy-Number and Segmental Duplication Maps using Next-Generation Sequencing (2009, unknown): “All loci were first masked for high copy common repeat elements (retroposons and short high copy repeats) using RepeatMasker 28, Tandem Repeats Finder29, and WindowMasker 30.”
• The UCSC Genome Browser database: 2015 update (2014, background): “Next, the chromosome sequences are analyzed for repetitive elements using RepeatMasker (A. F. A. Smit et al., RepeatMasker at http://repeatmasker.org) (54) WindowMasker (55) and Tandem Repeats Finder (56).”