I have a nucleotide sequence of a gene (short fragment) and I want to know which gene this sequence belongs to. Any suggestions?
How short is your gene fragment? Blast against NCBI database:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
Click on this link.
Enter your sequence and adjust your parameters based upon the your study type. Whether its a plant, human or microbial sequence. Once you get your blast result, look at your your query coverage score & identity score both should more than 90% provided your sequence length is more or equal to 200 bp.
This is fairly simple, you need to BLAST the gene sequence using "blastn".. "select somewhat similar sequences" for the result.
How long is your sequence?
The longer it is, the better confidence in prediction.
Better the confidence when more the Bitscore and %similarity and less the e-value and gaps.
Link is already provided to you by Yugendra, I will also give it here though,
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
You should have got it with the 3 precedent answers. Fill the form according to the case of your study.
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