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  • Problems with blastn execution from command line

    Hi all,
    I have the n-th problem with blast. This time it's blastn that is destroying my days..

    I use the blast+ (ncbi-blast-2.2.27+).

    I simply have downloaded an RFAM db and used makeblastd on it:

    with this command:

    ../ncbi-blast-2.2.27+/bin/makeblastdb -in rRNA.fa -dbtype 'nucl'

    and this output:
    Building a new DB, current time: 10/03/2012 11:30:22
    New DB name: rRNA.fa
    New DB title: rRNA.fa
    Sequence type: Nucleotide
    Keep Linkouts: T
    Keep MBits: T
    Maximum file size: 1000000000B
    Ignoring sequence 'lcl|149850' as it has no sequence data
    Adding sequences from FASTA; added 153329 sequences in 12.7754 seconds.



    So I created a nucleotide database for use with my fasta file. Queries are ATGC type.

    Then I run the blastn command on a file with 100 sequences:

    ../ncbi-blast-2.2.27+/bin/blastn -query longTestSeq.fasta -db data/rRNA.fa -out outBlastn100s



    And this is part of the outputfile:

    BLASTN 2.2.27+


    Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
    Miller (2000), "A greedy algorithm for aligning DNA sequences", J
    Comput Biol 2000; 7(1-2):203-14.
    Database: rRNA.fa
    153,329 sequences; 77,423,059 total letters

    Query= comp173253_c0_seq1
    Length=1717
    ***** No hits found *****
    Lambda K H
    1.33 0.621 1.12
    Gapped
    Lambda K H
    1.28 0.460 0.850
    Effective search space used: 123848567440

    Query= comp174620_c0_seq1
    Length=1566
    ***** No hits found *****

    Lambda K H
    1.33 0.621 1.12
    Gapped
    Lambda K H
    1.28 0.460 0.850
    Effective search space used: 113092217700

    ............and a lot of other NO HITS FOUND.

    Why this happens?

    I'm almost sure to have used the correct nucleotide database and queries. If you want I can cut and paste some of the sequences for each of them.

    Please help me!
    Thanks

  • #2
    Ok! There is nothing wrong! Now I know that since blastn is used to know about contaminations in the transcriptome... having NO HIT is meaning that my sequences doesn't.

    bye

    Comment

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