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.
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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: