Phigaro: high-throughput prophage sequence annotation

High Throughput Sequence Manipulation and Annotation

HAMR: high-throughput annotation of modified ribonucleotides.

RNA is often altered post-transcriptionally by the covalent modification of particular nucleotides; these modifications are known to modulate the structure and activity of their host RNAs. The recent discovery that an RNA methyl-6 adenosine demethylase (FTO) is a risk gene in obesity has brought to light the significance of RNA modifications to human biology. These noncanonical nucleotides, whe...

Simple high-throughput annotation pipeline (SHAP)

SUMMARY SHAP (simple high-throughput annotation pipeline) is a lightweight and scalable sequence annotation pipeline capable of supporting research efforts that generate or utilize large volumes of DNA sequence data. The software provides Grid capable analysis, relational storage and Web-based full-text searching of annotation results. Implemented in Java, SHAP recognizes the limited resources ...

A Web-based High-Throughput Tool for Next-Generation Sequence Annotation

The availability of a large number of genome sequences, resulting from inexpensive, high-throughput next-generation sequencing platforms, has created the need for an integrated, fully-automated, rapid, and high-throughput annotation capability that is also easy-to-use. Here, we present a web-based software application, Annotation of Genome Sequences (AGeS), which incorporates publicly-available...

EST-PAC HPC – a web portal for high-throughput EST annotation and protein sequence prediction

Expressed Sequence Tags (ESTs) are short DNA sequences generated by sequencing the transcribed cDNAs coming from a gene expression. They can provide significant functional, structural and evolutionary information and thus are a primary resource for gene discovery. EST annotation basically refers to the analysis of unknown ESTs that can be performed by database similarity search for possible ide...