Data workflow systems (DWFSs) enable bioinformatics researchers to combine components for data access and data analytics, and to share the final data analytics approach with their collaborators. Increasingly, such systems have to cope with large-scale data, such as full genomes (about 200 GB each), public fact repositories (about 100 TB of data) and 3D imaging data at even larger scales. As moving the data becomes cumbersome, the DWFS needs to embed its processes into a cloud infrastructure, where the data are already hosted. As the standardized public data play an increasingly important role, the DWFS needs to comply with Semantic Web technologies. This advancement to DWFS would reduce overhead costs and accelerate the progress in bioinformatics research based on large-scale data and public resources, as researchers would require less specialized IT knowledge for the implementation. Furthermore, the high data growth rates in bioinformatics research drive the demand for parallel and distributed computing, which then imposes a need for scalability and high-throughput capabilities onto the DWFS. As a result, requirements for data sharing and access to public knowledge bases suggest that compliance of the DWFS with Semantic Web standards is necessary. In this article, we will analyze the existing DWFS with regard to their capabilities toward public open data use as well as large-scale computational and human interface requirements. We untangle the parameters for selecting a preferable solution for bioinformatics research with particular consideration to using cloud services and Semantic Web technologies. Our analysis leads to research guidelines and recommendations toward the development of future DWFS for the bioinformatics research community.

BACKGROUND: Ribosome profiling (ribo-seq) provides experimental data on the density of elongating or initiating ribosomes at the whole transcriptome level that can be potentially used for estimating absolute levels of translation initiation at individual Translation Initiation Sites (TISs). These absolute levels depend on the mutual organisation of TISs within individual mRNAs. For example, according to the leaky scanning model of translation initiation in eukaryotes, a strong TIS downstream of another strong TIS is unlikely to be productive, since only a few scanning ribosomes would be able to reach the downstream TIS. In order to understand the dependence of translation initiation efficiency on the surrounding nucleotide context, it is important to estimate the strength of TISs independently of their mutual organisation, i.e. to estimate with what probability a ribosome would initiate at a particular TIS. RESULTS: We designed a simple computational approach for estimating the probabilities of ribosomes initiating at individual start codons using ribosome profiling data. The method is based on the widely accepted leaky scanning model of translation initiation in eukaryotes which postulates that scanning ribosomes may skip a start codon if the initiation context is unfavourable and continue on scanning. We tested our approach on three independent ribo-seq datasets obtained in mammalian cultured cells. CONCLUSIONS: Our results suggested that the method successfully discriminates between weak and strong TISs and that the majority of numerous non-AUG TISs reported recently are very weak. Therefore the high frequency of non-AUG TISs observed in ribosome profiling experiments is due to their proximity to mRNA 5'-ends rather than their strength. Detectable translation initiation at non-AUG codons downstream of AUG codons is comparatively infrequent. The leaky scanning method will be useful for the characterization of differences in start codon selection between tissues, developmental stages and in response to stress conditions.

MOTIVATION: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine-Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints. RESULTS: Here, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elongation of ribosome footprints at the 3'-end. It is likely that internal SD sequences induce a pause not on a single, but on several adjacent codons. This finding is important for our understanding of mRNA movement through the ribosome and also should facilitate interpretation of ribosome profiling data.

MOTIVATION: Conserved patterns across a multiple sequence alignment can be visualized by generating sequence logos. Sequence logos show each column in the alignment as stacks of symbol(s) where the height of a stack is proportional to its informational content, whereas the height of each symbol within the stack is proportional to its frequency in the column. Sequence logos use symbols of either nucleotide or amino acid alphabets. However, certain regulatory signals in messenger RNA (mRNA) act as combinations of codons. Yet no tool is available for visualization of conserved codon patterns. RESULTS: We present the first application which allows visualization of conserved regions in a multiple sequence alignment in the context of codons. CodonLogo is based on WebLogo3 and uses the same heuristics but treats codons as inseparable units of a 64-letter alphabet. CodonLogo can discriminate patterns of codon conservation from patterns of nucleotide conservation that appear indistinguishable in standard sequence logos. AVAILABILITY: The CodonLogo source code and its implementation (in a local version of the Galaxy Browser) are available at http://recode.ucc.ie/CodonLogo and through the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/.

MOTIVATION: RNA editing is a phenomenon, which is responsible for the alteration of particular nucleotides in RNA sequences relative to their genomic templates. Recently, a large number of RNA editing instances in humans have been identified using bioinformatic screens and high-throughput experimental investigations utilizing next-generation sequencing technologies. However, the available data on RNA editing are not uniform and difficult to access. RESULTS: Here, we describe a new database DARNED (DAtabase of RNa EDiting) that provides centralized access to available published data related to RNA editing. RNA editing locations are mapped on the reference human genome. The current release of the database contains information on approximately 42 000 human genome coordinates corresponding to RNA locations that undergo RNA editing, mostly involving adenosine-to-inosine (A-to-I) substitutions. The data can be queried using a range of genomic coordinates, their corresponding functional localization in RNA molecules [Exons, Introns, CoDing Sequence (CDS) and UnTranslated Regions (UTRs)] and information regarding tissue/organ/cell sources where RNA editing has been observed. It is also possible to obtain RNA editing information for a specific gene or an RNA molecule using corresponding accession numbers. Search results provide information on the number of expressed sequence tags (ESTs) supporting edited and genomic bases, functional localization of RNA editing and existence of known single nucleotide polymorphisms (SNPs). Editing data can be explored in UCSC and Ensembl genome browsers, in conjunction with additional data provided by these popular genome browsers. DARNED has been designed for researchers seeking information on RNA editing and for the developers of novel algorithms for its prediction. AVAILABILITY: DARNED is accessible at http://darned.ucc.ie

BACKGROUND: Ornithine decarboxylase antizymes are proteins which negatively regulate cellular polyamine levels via their affects on polyamine synthesis and cellular uptake. In virtually all organisms from yeast to mammals, antizymes are encoded by two partially overlapping open reading frames (ORFs). A +1 frameshift between frames is required for the synthesis of antizyme. Ribosomes change translation phase at the end of the first ORF in response to stimulatory signals embedded in mRNA. Since standard sequence analysis pipelines are currently unable to recognise sites of programmed ribosomal frameshifting, proper detection of full length antizyme coding sequences (CDS) requires conscientious manual evaluation by a human expert. The rapid growth of sequence information demands less laborious and more cost efficient solutions for this problem. This manuscript describes a rapid and accurate computer tool for antizyme CDS detection that requires minimal human involvement. RESULTS: We have developed a computer tool, OAF (ODC antizyme finder) for identifying antizyme encoding sequences in spliced or intronless nucleic acid sequenes. OAF utilizes a combination of profile hidden Markov models (HMM) built separately for the products of each open reading frame constituting the entire antizyme coding sequence. Profile HMMs are based on a set of 218 manually assembled antizyme sequences. To distinguish between antizyme paralogs and orthologs from major phyla, antizyme sequences were clustered into twelve groups and specific combinations of profile HMMs were designed for each group. OAF has been tested on the current version of dbEST, where it identified over six thousand Expressed Sequence Tags (EST) sequences encoding antizyme proteins (over two thousand antizyme CDS in these ESTs are non redundant). CONCLUSION: OAF performs well on raw EST sequences and mRNA sequences derived from genomic annotations. OAF will be used for the future updates of the RECODE database. OAF can also be useful for identifying novel antizyme sequences when run with relaxed parameters. It is anticipated that OAF will be used for EST and genome annotation purposes. OAF outputs sequence annotations in fasta, genbank flat file or XML format. The OAF web interface and the source code are freely available at http://recode.ucc.ie/oaf/ and at a mirror site http://recode.genetics.utah.edu/oaf/.

UNLABELLED: Correct annotation of genes encoding release factors in bacterial genomes is often complicated by utilization of +1 programmed ribosomal frameshifting during synthesis of release factor 2, RF2. In the absence of robust computational approaches for predicting ribosomal frameshifting, the success of proper annotation depends on annotators' familiarity with this phenomenon. Here we describe a novel computer tool that allows automatic discrimination of genes encoding class-I bacterial release factors, RF1, RF2 and RFH. Most usefully, this program identifies and automatically annotates +1 frameshifting in RF2 encoding genes. Comparison of ARFA performance with existing annotations of bacterial genomes revealed that only 20% of RF2 genes utilizing ribosomal frameshifting during their expression are annotated correctly. AVAILABILITY: The PHP based web interface of ARFA and the source code are located at http://recode.genetics.utah.edu/arfa