I sequenced a partial coding sequence (didn't run RACE) of a gene which got 800bp and the reference sequence got 1330bp. I have used bioinformatic tools such : Bioedit, Expasy, and ncbi orf finder, but got amino acid sequence of no homology on ncbi database, but the nucleotide sequence got homology when I ran Blast . Please how do I translate a gene having partial coding sequence?
The BLAST site has discussions under troubleshooting that may be helpful:
https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ
Find the section, "Troubleshooting", then go to "ERROR "No significant similarity found"
Hi Joseph
since you don't have the whole sequence of your RNA, you'll need to create the 3 possible frames for searching homologies in expasy.
all the best
fred
Since your nucleotide sequence has similarity with other known sequences in Blast search, translated amino acid sequences must have similarity if other near identical sequences are deposited in GenBank.
Expasy translate generates several open reading frame for any queried sequence and you have to pick up appropriate ORF merged in red color and started with Methionine.
Then do protein PSI Blast with your amino acid sequence weather it partial or full.
Thank you everyone thanks to @shin, Frederic and and Monju I have been able to translate the partial coding sequence using NCBI tBlasx search,and got regions of similarities with my sequence.