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  • visualization of blast/bowtie results in linux terminal

    Hi,
    I am looking for a simple and basic way/script to to see blast/bowtie results, not java based, just text..
    For example:
    Your best hit is
    query 0-----------------------------------100
    subject 35-----------------85

    any ideas?
    Thanks,
    Pap

  • #2
    BLAST output already is fairly visual. Below is a blastx result of mine.

    Code:
    Query= NODE_2_length_91_cov_18.516483
    
    Length=181
                                                                          Score     E
    Sequences producing significant alignments:                          (Bits)  Value
    
    ref|YP_002006372.1|  glycosyl transferase 2 [Cupriavidus taiwanen...   101    3e-24
    ref|YP_007084199.1|  putative O-linked N-acetylglucosamine transf...  47.8    1e-04
    [...]
    >ref|YP_002006372.1| glycosyl transferase 2 [Cupriavidus taiwanensis LMG 19424]
     emb|CAQ70309.1| putative Glycosyl transferase, family 2 [Cupriavidus taiwanensis
    LMG 19424]
    Length=393
    
     Score =  101 bits (251),  Expect = 3e-24, Method: Compositional matrix adjust.
     Identities = 47/59 (80%), Positives = 52/59 (88%), Gaps = 0/59 (0%)
     Frame = +3
    
    Query  3    TTNEDRISPEFAGEDSSRLKLLRPGEPLSAVDNFNLALSHATGEYLAFIGDDDLVSTQI  179
                T++EDRI+P FAG D +RLKLLRPGEPLS VDNFN ALSHA GEYLAFIGDDDL+S QI
    Sbjct  40   TSDEDRITPAFAGLDIARLKLLRPGEPLSVVDNFNFALSHARGEYLAFIGDDDLISPQI  98
    
    
    >ref|YP_007084199.1| putative O-linked N-acetylglucosamine transferase, SPINDLY family
    [Oscillatoria acuminata PCC 6304]
     gb|AFY80279.1| putative O-linked N-acetylglucosamine transferase, SPINDLY family
    [Oscillatoria acuminata PCC 6304]
    Length=2093
    
     Score = 47.8 bits (112),  Expect = 1e-04, Method: Compositional matrix adjust.
     Identities = 22/42 (52%), Positives = 29/42 (69%), Gaps = 0/42 (0%)
     Frame = +3
    
    Query  36   AGEDSSRLKLLRPGEPLSAVDNFNLALSHATGEYLAFIGDDD  161
                A  ++S++K  R  + LS  DN+ L LSHATGEY+  IGDDD
    Sbjct  51   ASFNNSKIKYYRAPQRLSMSDNWELGLSHATGEYIIIIGDDD  92
    As for bowtie, the output is in SAM. Direct viewing of SAM is probably not what you were thinking of; but there is samtools tview which might be what you are thinking of.
    Last edited by winsettz; 10-21-2013, 10:12 AM.

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