Development and implementation of CARAS algorithm for automatic annotation, visualization, and GenBank submission of chloroplast genome sequences

Yankai Li, Huan Li, Yingjie Zhu, Zhoujun Li, Chuntao Yin, Xiaohan Lin, Chang Liu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We present CARAS, a web server that allows the automatic annotation of a chloroplast genome sequence, and the visualization and editing of the annotation results interactively and in real-time. CARAS accepts a complete chloroplast genome sequence as input. First, it accurately predicts protein-coding sequences and exon-intron structures by combining the results from two types of annotation approaches: ab initio prediction algorithms and similarity based methods. Second, tRNA genes and inverted repeats are identified using tRNAscan and vmatch. Using 220 chloroplast genome sequences as test, we show that CARAS outperforms a similar application DOGMA overall. Third, the annotation results are presented as a circular map that includes the name, location, orientation, and length of the various features. A Flex-based module is implemented, allowing the users to add, delete, and edit the features on-line. The results are stored on the server and can be retrieved from a given URL. Users also have options to download the annotation results in GFF3 format for further analyses in other third party software tools or in JPEG format for publication. Finally, CARAS can be used to create a Sequin file for GenBank submission of the annotated genome sequence. CARAS is freely available at http://caras.bicoup.com, and it will significantly facilitate research work involving chloroplast genomes.

Original languageEnglish (US)
Title of host publication2012 Computing, Communications and Applications Conference, ComComAp 2012
Pages310-315
Number of pages6
DOIs
StatePublished - May 7 2012
Externally publishedYes
Event2012 Computing, Communications and Applications Conference, ComComAp 2012 - Hong Kong, China
Duration: Jan 11 2012Jan 13 2012

Other

Other2012 Computing, Communications and Applications Conference, ComComAp 2012
CountryChina
CityHong Kong
Period1/11/121/13/12

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Keywords

  • annotation
  • chloroplast genome
  • editing
  • visualization
  • web server

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Computer Science Applications

Cite this

Li, Y., Li, H., Zhu, Y., Li, Z., Yin, C., Lin, X., & Liu, C. (2012). Development and implementation of CARAS algorithm for automatic annotation, visualization, and GenBank submission of chloroplast genome sequences. In 2012 Computing, Communications and Applications Conference, ComComAp 2012 (pp. 310-315). [6154863] https://doi.org/10.1109/ComComAp.2012.6154863

Development and implementation of CARAS algorithm for automatic annotation, visualization, and GenBank submission of chloroplast genome sequences. / Li, Yankai; Li, Huan; Zhu, Yingjie; Li, Zhoujun; Yin, Chuntao; Lin, Xiaohan; Liu, Chang.

2012 Computing, Communications and Applications Conference, ComComAp 2012. 2012. p. 310-315 6154863.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Li, Y, Li, H, Zhu, Y, Li, Z, Yin, C, Lin, X & Liu, C 2012, Development and implementation of CARAS algorithm for automatic annotation, visualization, and GenBank submission of chloroplast genome sequences. in 2012 Computing, Communications and Applications Conference, ComComAp 2012., 6154863, pp. 310-315, 2012 Computing, Communications and Applications Conference, ComComAp 2012, Hong Kong, China, 1/11/12. https://doi.org/10.1109/ComComAp.2012.6154863
Li Y, Li H, Zhu Y, Li Z, Yin C, Lin X et al. Development and implementation of CARAS algorithm for automatic annotation, visualization, and GenBank submission of chloroplast genome sequences. In 2012 Computing, Communications and Applications Conference, ComComAp 2012. 2012. p. 310-315. 6154863 https://doi.org/10.1109/ComComAp.2012.6154863
Li, Yankai ; Li, Huan ; Zhu, Yingjie ; Li, Zhoujun ; Yin, Chuntao ; Lin, Xiaohan ; Liu, Chang. / Development and implementation of CARAS algorithm for automatic annotation, visualization, and GenBank submission of chloroplast genome sequences. 2012 Computing, Communications and Applications Conference, ComComAp 2012. 2012. pp. 310-315
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