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Translation initiation site databases | Transcription analysis

Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data.

Source text:
(Sparks and Brendel 2008) MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics.

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Presents carefully curated experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. The IRESite gradually evolved into a robust tool providing (i) biologically meaningful information regarding the IRESs and their experimental background (including annotation of IRES secondary structures and IRES trans-acting factors) as well as (ii) thorough concluding remarks to stored database entries and regularly updated evaluation of the reported IRES function. The database contents can be easily browsed using any web browser or searched for by an extremely powerful search interface which allows the search by a combination of multiple parameters.
It is based on the recently developed Global Translation Initiation sequencing (GTI-seq) technology, which provides global mapping of TIS codons at nearly single-nucleotide resolution. GTI-seq has the potential to reveal a comprehensive and unambiguous set of TIS codons across the entire transcriptome. TISdb provides tools to search for TIS positions and the associated open reading frames (ORFs) based on multiple GTI-seq datasets. Some filters are available to gain different reliability of the results. Flexible search engine offers different input format. Result output includes table coordinates and images for easy visualization.
HCVIVdb / HCV IRES variation database
Focuses on the reported variations of the hepatitis C virus (HCV) internal ribosomal entry site (IRES) that have been found in patients and/or purposely introduced to the viral genome and on the impact of these variations on HCV IRES activity. HCVIVdb offers insight into the functional significance of the HCV IRES domains, subdomains, regions and even individual nucleotides. The design of the database permits users to access, analyze and download relevant information through the sophisticated but user-friendly graphical interface. HCVIVdb is mainly dedicated to detailed comparative and functional analysis of all the HCV IRES domains, which can further lead to the development of site-specific drug designs and provide a guide for future experiments.
HAltORF / Human Alternative Open Reading Frames
Allows investigation in the human transcriptome of alternative Open Reading Frames (AltORFs) overlapping with annotated coding sequence (CDS), and putatively expressed by out-of-frame alternative translation initiation (ATI). HAltORF is a web-based searchable database containing more than 17 0000 distinct predicted AltORFs in the CDS of 31 422 mRNAs transcribed from 8744 genes. Users can search by gene name or symbol, mRNA or protein GenBank accession number, and by protein sequence. The database can be downloaded in Microsoft Excel or FASTA format.
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