ArticleNucleic acids research2009
TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 37 citations in OpenAlex.
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- Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing ofProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Comparative analysis of miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species.BMC plant biology · 2019Article
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- The maize W22 genome provides a foundation for functional genomics and transposon biology.Nature genetics · 2018Article
- Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower.The Plant cell · 2017Article
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- Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements.Molecular biology and evolution · 2016Article
- MuTAnT: a family of Mutator-like transposable elements targeting TA microsatellites in Medicago truncatula.Genetica · 2015Article
- Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- MnTEdb, a collective resource for mulberry transposable elements.Database : the journal of biological databases and curation · 2015Article
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- Losing identity: structural diversity of transposable elements belonging to different classes in the genome of Anopheles gambiae.BMC genomics · 2012Article
- Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains.Plant cell reports · 2012Article
- The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Gene families compose a large proportion of eukaryotic genomes. The rapidly expanding genomic sequence database provides a good opportunity to study gene family evolution and function. However, most gene family identification programs are restricted to searching protein databases where data are often lagging behind the genomic sequence data. Here, we report a user-friendly web-based pipeline, named TARGeT (Tree Analysis of Related Genes and Transposons), which uses either a DNA or amino acid 'seed' query to: (i) automatically identify and retrieve gene family homologs from a genomic database, (ii) characterize gene structure and (iii) perform phylogenetic analysis. Due to its high speed, TARGeT is also able to characterize very large gene families, including transposable elements (TEs). We evaluated TARGeT using well-annotated datasets, including the ascorbate peroxidase gene family of rice, maize and sorghum and several TE families in rice. In all cases, TARGeT rapidly recapitulated the known homologs and predicted new ones. We also demonstrated that TARGeT outperforms similar pipelines and has functionality that is not offered elsewhere.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.