I have a partial amplified sequence of a gene cluster. Is that advisable to BLAST against a draft genome. Can we report in publication. My sequence similarity is more when i BLAST against strain genome which is available as draft rather than representative genomes.
Yes, you can blast against a draft genome, and that may be sufficient for what you want, as long as enough of your sequence is covered in the blast results. I'm not sure what you want to report in your publication, but it might be worth (although a bit of work) doing multiple alignments (using clustalw or other) between your sequence, a region of the draft genome of your strain that you think corresponds to your sequence, and orthologous regions of the other representative genomes.
Yes, you can do it using local version of blast
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
Yes, do it using local BLAST as suggested by others. Another option is to use USEARCH for local BLASTing etc. It's supposed to be faster for large dataset which you seem to have.
And you may also do locally from the command prompt the alignments using ClustalW (or the latest version Clustal Omega).
http://www.clustal.org/omega/
http://drive5.com/usearch/manual/
For whole genome comparisons, Mummer or Synmap might give you more relevant results.
https://genomevolution.org/wiki/index.php/SynMap
http://mummer.sourceforge.net
You can go to BLASTn
1) Enter query sequence
2) Upload file of draft genome in subject sequence
Perform BLAST you will get the result.
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