I am trying to find the genes associated with my fasta sequences.I found these sequences from main ucsc genome browser.Are there any alternatives to using http://great.stanford.edu/ as it is not showing the genes associated with the genes nor the Gene Ontology.
If you extracted fasta sequences from the UCSC Table Browser, then the associated genes and other attributes might also be available from that source – it depends on what those sequences represent. If you are not sure how to construct a query, review the guide then write to their support team. Both are under the Help menu here: http://genome.ucsc.edu/
These Galaxy tutorials will likely be of interest if your goal is analysis instead: