CpGAVAS statistics

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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 Yes

Maintainer


  • person_outline Chang Liu <>

Publication for CpGAVAS

CpGAVAS in pipeline

2015
PMCID: 4599086
PMID: 26450727
DOI: 10.1128/genomeA.01151-15

[…] instructions. a paired-end approach with a read size of ~100 bp was employed. sequence assembly was performed with soapdenovo2 software version 2.01 (). all open reading frames were annotated using cpgavas () and mitofy () for chloroplast and mitochondrial genomes, respectively., the p. crispa plastid genome (cpdna) information resides on a single molecule with a total length of 196,502 bp […]


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CpGAVAS in publications

 (28)
PMCID: 5916314
PMID: 29721304
DOI: 10.1002/ece3.3989

[…] , table s6). genetic diversity for the whole chloroplast calculated using dnasp software (rozas, sánchez‐delbarrio, messeguer, & rozas, )., 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 […]

PMCID: 5861152
PMID: 29593773
DOI: 10.3389/fpls.2018.00324

[…] extracted and subjected to next-generation sequencing. the cp genome was then assembled, and the gaps were filled using pcr amplification and sanger sequencing. genome annotation was conducted using cpgavas web server. the genome was 144,133 bp in length, presenting a typical quadripartite structure of large (lsc; 91,666 bp) and small (ssc; 17,328 bp) single-copy regions separated by a pair […]

PMCID: 5877562
PMID: 29494509
DOI: 10.3390/ijms19030701

[…] performed on these chloroplast reads. overlapping contigs of one or more assemblies were used to assemble the complete cpdna sequence., 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 […]

PMCID: 5732391
PMID: 29246263
DOI: 10.1186/s13104-017-3077-8

[…] (ir) regions (27,256 bp each), a large single-copy (lcs) region (87,444 bp) and a small single-copy (ssc) region (18,065 bp). the overall gc content is 37.23%. genome annotation using dogma [] and cpgavas [] with phoenix dactylifea [] as a reference and trnas prediction using trna-scanse [] provided that the cp genome contains 113 unique genes: 79 protein-coding genes, 30 trna genes, and four […]

PMCID: 5701465
PMID: 29167240
DOI: 10.1128/genomeA.01150-17

[…] version 2.2.0 (). the complete chloroplast genome sequence was then assembled with the mira version 4.9.6 software (). the protein-, rrna-, and trna-coding genes were annotated using dogma, cpgavas, and trnascan-se 2.0, respectively (). manual editing was also carried out by comparison with the chloroplast genome sequence of chenopodium species deposited in ncbi genbank. the circular […]


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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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