A transfer RNA database. tRNADB-CE was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. One important characteristic of tRNADB-CE is inclusion of tRNAs found in a large number of partially sequenced genomes.
Provides overview statistics of tRNA genes within each analyzed genome, including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments. Direct links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of tRNA genes in the context of all other local genetic information. The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group.
Identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. The website Islander presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.
Offers data about mammalian mitochondrial tRNA sequences. mitotRNAdb allows implementation and validation of algorithms and can process to automated nucleic acid data transfer. It combines tRNA gene sequences and classifies them in two categories: ‘Genomic tRNA Compilation’ and ‘Compilation of tRNA Genes’. The database includes tRNA-like structures (TLSs) encoded in viruses and phages.
Contains currently more than 12,000 tRNA genes from 577 species and 623 tRNA sequences from 104 species, classified into families according to amino acid specificity as defined by anticodon triplets. tRNAdb provides various services including graphical representations of tRNA secondary structures, a customizable output of aligned or un-aligned sequences with a variety of individual and combinable search criteria, the construction of consensus sequences for any selected set of tRNAs, as well as the illustration of consensus and derived typical cloverleaf structures with features of conservation for any selected set of tRNAs.
Compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. This includes 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included.
Displays static individual 2D structures of human mitochondrial tRNA genes with location of polymorphisms and pathology-related point mutations. Mamit-tRNA is a database for mammalian mitochondrial genomes and has been developed for deciphering structural features of mammalian mitochondrial tRNAs. The database is expected to facilitate exploration of structure/function relationships of mitochondrial tRNAs and to assist clinicians in the frame of pathology-related mutation assignments.
A resource for researchers studying Listeria and related organisms. The L. monocytogenes 10403S BioCyc database allows users to (i) have a comprehensive view of all reactions and pathways predicted to take place within the cell in the cellular overview, as well as to (ii) upload their own data, such as differential expression data, to visualize the data in the scope of predicted pathways and regulatory networks and to carry on enrichment analyses using several different annotations available within the database.
Facilitates comparative analysis of Listeria spp. ListeriaBase currently houses 850,402 protein-coding genes, 18,113 RNAs and 15,576 tRNAs from 285 genome sequences of different Listeria strains. It aims to be one-stop genomic resource and analysis platform where useful genomic data and information can be obtained and analyzed using the provided analysis tools. The database provides a real-time search engine to facilitate seamless search capability.
Stores and retrieves complete set of tRNA sequences in all archaeal species and primitive eukaryotic species to promote the next study of tRNA evolution and tRNA processing. SPLITSdb contains 3,741 sequences and secondary structures of various types of tRNA genes and 783 sequences and secondary structures of tRNA introns.
Developed with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations.