If the database of a particular plant with a specific gene is not available on NCBI, what is the best way to do a BLAST of the received sequence after sequencing?
There are some other databases also, so maybe you can blast it there. Here is the link:
http://www.molbiol-tools.ca/Homology.htm
Hi Raksha
You have few options in such cases:
1) You can look into EST databases with query restricted to your plant, species, genus etc. of interest
2) you can also make a local database of sequences of your organism of interest and use it regulary for BLAST analysis
bye
If particular plant gene sequence is not available in NCBI database then u can BLAST with other plant of same family or genus. At the same time you can search for which trait actually looking for and compare it with sequence of it. Even from gene sequence translate it into amino acid/protein sequence and go for protein BLAST which will give more accurate result/prediction with gene of interest. This will give the idea of length of Amino acid and presence of intron is less or more.
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