i am working on two fruit varieties and their differemt gene expression profile such as genes in volves in fruit cuticle wax biosynthesis. as according to references i have found some KCS, CER, MYB families gene involve in cuticle wax biosynthesis.but when i blast query (cds seq ) of 25 genes into my subject (transcriptome , Seq), i have not found any matching of bit score in it.
1–whats your suggestion about that ?
2–can you recommend me more genes about cuticle wax biosynthesis. :
You can extract the full length sequences (complete orf) of your targeted/selected 25 genes from the RNA-Seq data and then subject them for homology search using BLASTx. You can use NCBI nr and swissprot/uniprot database to find the homologous sequences.
Hope this may help you to find you the best annotation for you sequences.
Romit Seth Dear Sirm
i have tried using the bioeidt and tbtool for blasting, but i have not the homologous so what shoud do?
Dear Hafiz Muhammad Rizwan
If you are unable to find homologues of any of those genes from any of the public protein data bases available then probably they may be your novel genes.
Dear Romit Seth
if i not found the BLAST by using them as Subject, so you mean that maybe they are Novel genes? But i have selected those Gene Sequences from Arabidopsis, so how will deal with them and what about in designing the primers ? can you please explain
Thanks
Dear Hafiz Muhammad Rizwan
I think you need to select your your sequences based their annotation with TAIR/ swissprot/ nr public protein databases. You can also consider percent identity and query coverage to identify the functional region in your case. For primer designing you can use Batch primer 3 software, I am attaching the link below.
http://batchprimer3.bioinformatics.ucdavis.edu/cgi-bin/batchprimer3/batchprimer3.cgi
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