CpGAVAS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CpGAVAS
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Tool usage distribution map

This map represents all the scientific publications referring to CpGAVAS per scientific context
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Associated diseases

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Popular tool citations

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Protocols

CpGAVAS specifications

Information


Unique identifier OMICS_08008
Name CpGAVAS
Interface Web user interface
Restrictions to use None
Input data Complete chloroplast genome sequence
Output data The annotation results in GFF3 format can be edited using any compatible annotation editing tools.
Output format GFF3
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publications for CpGAVAS

CpGAVAS citations

 (39)
call_split

The chloroplast genome of Cerasus humilis: Genomic characterization and phylogenetic analysis

2018
PLoS One
PMCID: 5919044
PMID: 29694421
DOI: 10.1371/journal.pone.0196473
call_split See protocol

[…] ]. Three software were used for genome degenerate base correction, namely, bwa, samtools, and bcftools [,]. The complete C. humilis chloroplast genome sequence was annotated using the online software CpGAVAS developed by Liu et al [] (http://www.herbalgenomics.org/0506/cpgavas/analyzer/annotate). TRNAscan-SE was used in tRNA confirmation []; http://lowelab.ucsc.edu/tRNAscan-SE/). Genomic circle gr […]

library_books

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

2018
PLoS One
PMCID: 5919006
PMID: 29694416
DOI: 10.1371/journal.pone.0196069

[…] aining genes or genes with short exons such as petB, and dealing with trans-splicing reading frames like rps12 is challenging with DOGMA. Moreover DOGMA [] generates a special output file compared to CpGAVAS [] or GeSeq [], which generate standard general feature format (.gff) or GenBank (.gb) files that can be integrated with other software without further processing. From the currently available […]

library_books

Diversity and evolution of rice progenitors in Australia

2018
Ecol Evol
PMCID: 5916314
PMID: 29721304
DOI: 10.1002/ece3.3989

[…] All chloroplast sequences were annotated using the CpGAVAS website (http://www.herbalgenomics.org/0506/cpgavas/analyzer/home), using the default parameters as recommended. The outcome was imported directly into Geneious software to allow comparison wi […]

call_split

Sequencing and Analysis of Strobilanthes cusia (Nees) Kuntze Chloroplast Genome Revealed the Rare Simultaneous Contraction and Expansion of the Inverted Repeat Region in Angiosperm

2018
Front Plant Sci
PMCID: 5861152
PMID: 29593773
DOI: 10.3389/fpls.2018.00324
call_split See protocol

[…] tained 25 μL of Taq MasterMix (2 × ), 2 μL of forward primer (10 μM), 2 μL of reverse primer (10 μM), and purified cp DNA ( < 1 μg). RNase-free water was added to a final reaction volume of 50 μL.The CpGAVAS web service () was used to annotate the S. cusia cp genome. Cutoffs for the E-values of BLASTN and BLASTX were 1e-10. The number of top hits to be included in the reference gene sets for annot […]

library_books

Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses

2018
Int J Mol Sci
PMCID: 5877562
PMID: 29494509
DOI: 10.3390/ijms19030701

[…] Draft annotations were generated with the web-based software CPGAVAS [,] to check gene content and order. These draft annotations were corrected where necessary, guided by alignments to other well-characterized eudicot plastomes including those of Arabidopsis t […]

library_books

Complete chloroplast genome of the medicinal plant Amomum compactum: gene organization, comparative analysis, and phylogenetic relationships within Zingiberales

2018
PMCID: 5811967
PMID: 29449878
DOI: 10.1186/s13020-018-0164-2

[…] Preliminary gene annotation of this cp genome was performed by CpGAVAS, a program available online (http://www.herbalgenomics.org/0506/cpgavas) []. The position of each gene was then manually corrected by Apollo [] after alignment to the reference genomes by MEGA […]


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CpGAVAS institution(s)
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
CpGAVAS funding source(s)
This work was supported by a start fund from the Chinese Academy of Medical Science (No. 431118) granted to C. Liu, Basic Scientific Research Operation Grants for State-Level Public Welfare Scientific Research Initiatives (No. YZ-12-04 granted to C. Liu), Research grant for returned Overseas Chinese Scholars, Ministry of Human Resources (No. 431207) granted to C. Liu, a grant from National Science Foundation (No. 81202859) to HM. Chen and Program for Changjiang Scholars and Innovative Research Team in University of Ministry of Education of China (No. IRT1150).

CpGAVAS reviews

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Shuangyan Ru

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ZHA XI

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