I am working on fruit cuticle wax biosynthesis and did the transcriptome and now I have collected many genes from different sources such as from articles and online etc, for example, CER1, CER3, KCS, etc which i will use for further qPCR.
But how can i make sure that these genes are identified and that genes are specific for wax? as because of according to reference one gene perform different functions.
sequence your sample, file convert to blast format, then use different online software for find out different gene .
https://blast.ncbi.nlm.nih.gov/Blast.cgi
To help you Hafiz Muhammad Rizwan, I need to know: what tissue did you sampled for sequencing?
you can check on NCBI blast.
Simple copy the sequence of gene from transcriptom data and past in blast on NCBI. https://blast.ncbi.nlm.nih.gov/Blast.cgi
Mohammed Shaker Hossain can you recommend me some softwares for file converting and softwares for find out different gene
Ali Raza Jahejo Could you please explain about the fold changes?
Francis Nunes I have used passion fruit two different varieties at harvesting stage and Peel was used as sample for Seq
Abid Ali Soomro directly BLAST or need to specify the Min and Max ranges ?
Dear Hafiz Muhammad Rizwan , thank you for send info. Once you are looking for fruit cuticle wax biosynthesis, I think their choices and decisions were the best ones, since a higher production of these substances (wax) in the fruit peel is expected in the harvest phase. Of course not all genes expressed in the fruit peel encode proteins/enzymes for wax synthesis. But your strategy (RNA-Seq from peel and probably adjacent internal/lined tissues) represents an important filter that will facilitate the next gene identification steps. Thus, after using Blast (preferably BlastX or BlastP), recover the IDs of the main orthologs to perform analyses of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes). These analyses of functional enrichment and metabolic pathways may indicate which genes are annotated inside some (wax-related) GO terms and/or some (wax-related) KEGG pathways.
Dear Francis Nunes Thanks a lot for your nice sharing,
i will proceed accordingly and if have further question then will keep in contact
Dear Hafiz Muhammad Rizwan ,
check these two articles (mainly "functional annotation" sections):
Identification of candidate genes involved in wax deposition in Poa pratensis by RNA-seq
Article Identification of candidate genes involved in wax deposition...
RNA-Seq Reveals Leaf Cuticular Wax-Related Genes in Welsh Onion
Article RNA-Seq Reveals Leaf Cuticular Wax-Related Genes in Welsh Onion
Best,
Francis
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