Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Advancing Precision Medicine for Rare Diseases in Children
      by seqadmin




      Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...
      12-16-2024, 07:57 AM
    • seqadmin
      Recent Advances in Sequencing Technologies
      by seqadmin



      Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.

      Long-Read Sequencing
      Long-read sequencing has seen remarkable advancements,...
      12-02-2024, 01:49 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 12-17-2024, 10:28 AM
    0 responses
    26 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 12-13-2024, 08:24 AM
    0 responses
    42 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 12-12-2024, 07:41 AM
    0 responses
    28 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 12-11-2024, 07:45 AM
    0 responses
    42 views
    0 likes
    Last Post seqadmin  
    Working...
    X