Corresponding author: H Alexander Ebhardt

Extending microRNAs

Motivation

MicroRNAs (miRNAs) are short RNA sequences, in miRBase these sequences range from 16 to 35 nucleotides. Of all the identified sequences, the majority of miRNAs are 21 or 22 nucleotides in length. Despite the range of sequence lengths for different miRNAs, individual miRNAs are reported as a specific sequence of a particular length. A recent report describing a longer variant of a previously identified miRNA in Arabidopsis thaliana has prompted this investigation for variations in length of other miRNAs. Ebhardt HA, Fedynak A, Fahlman RP.: Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity. Silence 2010 1:12.

Ebbie-(mis)match v4.3

Motivation

Recent advances in DNA sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here, we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous non-identical small RNA sequences. Investigating the sites and identities of substitution errors reveal that many potentially originate as a result of post transcriptional modifications or RNA editing. From the datasets, examples of tRNA and micro RNA are identified. Modifications include N1-methyl modified purine nucleotides in tRNA, potential deamination or base substitutions in micro RNAs, 3' micro RNA uridine extensions and 5' micro RNA deletions. Additionally, further analysis of large sequencing datasets reveal that the combined effects of 5' deletions and 3' uridine extensions can alter the specificity by which micro RNAs associate with different Argonaut proteins. Hence, we demonstrate that not all sequencing errors in small RNA datasets are technical artifacts, but that these actually often reveal valuable biological insights to the sites of post transcriptional RNA modifications.

For complete description of Ebbie-(mis)match, please see the accompanying publication in Nucleic Acids Research - 2009 May;37(8):2461-70..

Availability

Ebbie-(mis)match-AGO v1

Motivation

For complete description of Ebbie-(mis)match-AGO, please see the accompanying publication in Nucleic Acids Research - Epub Mar 2, 2009.

Availability

Ebbie v3.0.9

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server.

Motivation

Sequencing projects, such as cloning of small RNAs, result in thousands of sequencing files. Here we describe an automated analysis pipeline, which excises the cloned RNA; uses BlastN to search it against various databases and allows standardized annotation using cgi-scripts. After annotating the new clone, the sequence and its annotation are stored in a MySQL database as well as in a flat file for subsequent BlastN searches. This sequence analysis pipeline eliminates manual mistakes, allows the discovery of multiply cloned sequences and reliably stores sequences and their annotations.

For complete description of Ebbie, please see the accompanying publication in BMC Bioinformatics 7:185.

Availability

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