SeqAnt 2.0: Whole-Genome Annotation and Natural-Language Searching in the Cloud

CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation

Motivation Homology-based gene prediction is a powerful concept to annotate newly sequenced genomes. We have previously demonstrated that whole genome alignments can be utilized for accurate comparative coding gene annotation. Results Here we present CESAR 2.0 that utilizes genome alignments to transfer coding gene annotations from one reference to many other aligned genomes. We show that CES...

SeqAnt 2012: Recent Developments in Next-Generation Sequencing Annotation

The Effects of Multimedia Annotations on Iranian EFL Learners’ L2 Vocabulary Learning

In our modern technological world, Computer-Assisted Language learning (CALL) is a new realm towards learning a language in general, and learning L2 vocabulary in particular. It is assumed that the use of multimedia annotations promotes language learners’ vocabulary acquisition. Therefore, this study set out to investigate the effects of different multimedia annotations (still picture annotatio...

Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG

SUMMARY Circleator is a Perl application that generates circular figures of genome-associated data. It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output. It is designed to be both flexible and easy to use. It includes a library of circular track types and predefined configuration files for common use-cases, including. (i) visu...

Multimedia Annotation: Comparability of Gloss Modalities and their Implications for Reading Comprehension

This study compared the effects of two annotation modalities on the reading comprehension of Iranian intermediate level EFL learners. The two experimental groups under study received treatment on 10 academic L2 reading passages under one of two conditions: One group received treatment on key words in the reading passages through a multimedia environment providing textual annotations. The second...