How to find all chloroplast genes from SNP data of whole genome of 200 rice accession??

Question

[naveedkhanchemist]

Hello Buddies,

I am new in bioinformatics. I got a task from my seniors. I have all SNPs list of 200 rice manicure set. I have to make a list of all genes present in chloroplast in my rice manicure set. How I can generate that list using SNP data. The manicure set contain Japonica and Indica species both....

[natasha.sernova]

See these posts:

Downloading rice chloroplast genome

How To Annotate Parts Of Chloroplast Dna?

See also these papers:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201551/

Direct Chloroplast Sequencing: Comparison of Sequencing Platforms and Analysis Tools for Whole Chloroplast Barcoding

Whole-Genome Resequencing and Transcriptomic Analysis to Identify Genes Involved in Leaf-Color

Diversity in Ornamental Rice Plants

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405343/

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of

genome-wide discovery of single-nucleotide polymorphisms.

http://sra.dbcls.jp/search/view/DRP000010

There is a current rice database:

http://pcp.oxfordjournals.org/content/early/2016/01/15/pcp.pcv171.full