ArticleNucleic acids research2013
GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Article
- Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Programmed Deviations of Ribosomes From Standard Decoding in Archaea.Frontiers in microbiology · 2021Review
- Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.Nucleic acids research · 2016Review
- High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus.Scientific reports · 2016Article
- Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning.Nature reviews. Genetics · 2015Review
- Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli.Nucleic acids research · 2014Article
- Identification of the nature of reading frame transitions observed in prokaryotic genomes.Nucleic acids research · 2013Article
Corrections and comments
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3 authors.
Funding
Abstract
Database annotations of prokaryotic genomes and eukaryotic mRNA sequences pay relatively low attention to frame transitions that disrupt protein-coding genes. Frame transitions (frameshifts) could be caused by sequencing errors or indel mutations inside protein-coding regions. Other observed frameshifts are related to recoding events (that evolved to control expression of some genes). Earlier, we have developed an algorithm and software program GeneTack for ab initio frameshift finding in intronless genes. Here, we describe a database (freely available at http://topaz.gatech.edu/GeneTack/db.html) containing genes with frameshifts (fs-genes) predicted by GeneTack. The database includes 206 991 fs-genes from 1106 complete prokaryotic genomes and 45 295 frameshifts predicted in mRNA sequences from 100 eukaryotic genomes. The whole set of fs-genes was grouped into clusters based on sequence similarity between fs-proteins (conceptually translated fs-genes), conservation of the frameshift position and frameshift direction (-1, +1). The fs-genes can be retrieved by similarity search to a given query sequence via a web interface, by fs-gene cluster browsing, etc. Clusters of fs-genes are characterized with respect to their likely origin, such as pseudogenization, phase variation, etc. The largest clusters contain fs-genes with programed frameshifts (related to recoding events).
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