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GV / GeneValidator

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Automatically identifies problematic gene predictions and to aid manual curation. For each gene, GV performs multiple analyses based on comparisons to gene sequences from large databases. The resulting report identifies problematic gene predictions and includes extensive statistics and graphs for each prediction to guide manual curation efforts. GV thus accelerates and enhances the work of biocurators and researchers who need accurate gene predictions from newly sequenced genomes.

GtRNAdb / Genomic tRNA Database

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.

MINTmap / MItochondrial and Nuclear TRF mapping

Identifies the subset of discovered transfer RNA fragments (tRFs) that could be originating outside of tRNA space and flags them as candidate false positives. MINTmap is a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNAseq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs.

tRNAdb / Transfer RNA database

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.

PlantRNA

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.