I am running command line blastn with a local copy of a microbial database. My command looks like
blastn -query query.txt -db 16SMicrobial -out newres.txt -wordsize 11 -evalue 10 -gapextend 2 -gapopen 5 -penalty -3 -reward 1 This gives me 81 hits, they all have the same score such as
Sequences producing significant alignments: Score (Bits) E Value
ref|NR042397.1| Dokdonella fugitiva strain : A3 16S ribosomal R... 28.2 6.3
ref|NR041093.1| Streptomyces rubiginosohelvolus strain NBRC 129... 28.2 6.3
ref|NR041539.1| Kitasatospora kazusensis strain SK60 16S riboso... 28.2 6.3
ref|NR041538.1| Kitasatospora saccharophila strain SK15 16S rib... 28.2 6.3
ref|NR_044150.1| Streptomyces omiyaensis strain NRRL B-1587 16S ... 28.2 6.3
...
Isn't that strange?
Further, I repeated the query(same parameters) on the NCBI website, and that gave 162 hits. e.g.
NC017551.1 Leptospira interrogans serovar Lai str. IPAV chromosome chromosome 1, complete sequence 398 398 100% 1e-108 100%
NC008463.1 Pseudomonas aeruginosa UCBPP-PA14 chromosome, complete genome 398 398 100% 1e-108 100%
NC_002516.2 Pseudomonas aeruginosa PAO1 chromosome, complete genome 398 398 100% 1e-108 100%
I tried to compare the two, e.g. I looked for "Kitasatospora " from the former in the latter set of results, and could not find any matches. What am I doing wrong ?!
Even when you re-do on NCBI, the score and E-value are same, aren't they? But I think you should consider to update your local database for blast+~