GeSeq – versatile and accurate annotation of organelle genomes

By Michael Tillich, Pascal Lehwark, Tommaso Pellizzer, Elena S. Ulbricht-Jones, A. Fischer, Ralph Bock, Stephan Greiner. Nucleic Acids Res., 2017

2,822 citations recorded by the source corpus.

Abstract We have developed the web application GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) for the rapid and accurate annotation of organellar genome sequences, in particular chloroplast genomes. In contrast to existing tools, GeSeq combines batch processing with a fully customizable reference sequence selection of organellar genome records from NCBI and/or references uploaded by the user. For the annotation of chloroplast genomes, the application additionally provides an integrated database of manually curated reference sequences. GeSeq identifies genes or other feature-encoding regions by BLAT-based homology searches and additionally, by profile HMM searches for protein and rRNA coding genes and two de novo predictors for tRNA genes. These unique features enable the user to conveniently compare the annotations of different state-of-the-art methods, thus supporting high-quality annotations. The main output of GeSeq is a GenBank file that usually requires only little curation and is instantly visualized by OGDRAW. GeSeq also offers a variety of optional additional outputs that facilitate downstream analyzes, for example comparative genomic or phylogenetic studies.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/90721248756b66f629b73ec1e96ee0a0553c2c13

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Chang Liu
2. Haimei Chen
3. Linchun Shi
4. Jing Tang

In Molecular Biology

1. Chang Liu
2. Peter Poczai
3. Haimei Chen
4. Ali Amiryousefi
5. Linchun Shi
6. Jing Tang
7. Jaakko Hyvönen
8. Shuyu Zheng

Citations in the corpus

• CPGView: A package for visualizing detailed chloroplast genome structures (2023, neutral): “…these tools include DOGMA (Wyman et al., 2004), CPGAVAS (Liu et al., 2012), Plann (Huang & Cronk, 2015), Verdant (McKain et al., 2017), GeSeq (Tillich et al., 2017 ), AGORA (Jung et al., 2018), OrganellarGenomeDRAW version 1.3.1 (OGDRAW) (Lohse et al., 2013), CPGAVAS2 (Shi et al., 2019), and…”
• CPGAVAS2, an integrated plastome sequence annotator and analyzer (2019, methodology): “About two, eleven, five, eleven and thirteen genes had incorrect start or end positions predicted by CPGVAS2, AGORA, GeSeq, MFannot and DOGMA, respectively.”
• Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes (2020, methodology): “…solely optimized for assembling (GetOrganelle: Jin et al., 2019; FastPlast: McKain and Wilson, 2017; MITObim: Hahn et al., 2013), annotating (Plann: Huang and Crong, 2015; MITOS: Bernt et al., 2013), and analyzing organelle genomes (Chlorobox: Tillich et al., 2017; CPGAVAS2: Shi et al., 2019).”