in reply to blast crashed

[blastall] WARNING: Unable to open TCV-jagger.fna.nin
This error seems to indicate that there is a problem with the nin file, which is one of the index files required by the blastall program. Try recreating the index files using the formatdb command (if you didn't create them in the first place, that would be the problem).

You should have some local documentation with the program. In addition, here are a couple of links that might help.

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Re^2: blast crashed
by Anonymous Monk on Mar 26, 2008 at 16:53 UTC
    oh thanks very much for your help.
    I thas been sorted. Now, while working on to get the result of Blast I would like to get the start and end position of the query sequence along the databas(large sequence)
    For example
    let the query sequence be
    ATG
    GTC
    and the large sequence be
    ATGCCCCGTC
    The hit position of the first sequence will be start :1 and end: 3
    And the second sequence will be start:3 and end: 6
    Again the second sequence matches at start8: and end 11 I looked at Hsp but the start and end in it gives just the start and end of the query
    Any suggestions
    Thanks