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  • lindenb
    replied
    Save your blast result as XML and process it with a XSLT stylesheet.

    Examples:

    * http://www.biostars.org/p/6635/

    * http://www.biostars.org/p/85258/

    Leave a comment:


  • gringer
    replied
    Use a different output format (ASN, CSV, or XML). The default text-based format is only meant to be for viewing, not data manipulation, and can change without notice.

    Leave a comment:


  • Genomics101
    started a topic Reformatting BLAST+ pairwise alignment?

    Reformatting BLAST+ pairwise alignment?

    Greetings!

    The default for BLAST+ output is a pairwise alignment broken up into 60bp increments:

    Code:
    Query  1     TTATTTTTCTTGATAGAATTAATTCTAATATTAGCACATTAAAAAATACTAAGTC-AAAT  59
                 ||||||| ||||||||  |||||| |||||||| |||||||||||||| |||||| ||||
    Sbjct  542   TTATTTTGCTTGATAGCGTTAATTATAATATTACCACATTAAAAAATATTAAGTCAAAAT  601
    
    Query  60    TGTAATATTTCATTTGATATTGTATGCATACAATTTT-ATC---T--TACCTTTAAGAAT  113
                 ||||||||||||||||||  ||||||||||||||||| |||   |  ||||||||| |||
    Sbjct  602   TGTAATATTTCATTTGAT-CTGTATGCATACAATTTTAATCTTATCATACCTTTAATAAT  660
    
    Query  114   ATGTATAA-TAATTTATACCCATGTAGTT-TATTAAAT--A-AACAT-ATTTGTGCGTAT  167
                 |||||||| |||| |||| | | ||| |   || ||||  |    || |||| | |||||
    Sbjct  661   ATGTATAATTAATATATATCAACGTATTCGAATCAAATGGATTTAATGATTTTTTCGTAT  720
    
    Query  168   CCAATGCGTTTATCTATTGTTATTACTA-T--TA-T--TATTGTTACTGCTATATCACTG  221
                   ||| |||||||||||||||||||||| |  || |  |||| ||| ||| || ||||||
    Sbjct  721   TTAATACGTTTATCTATTGTTATTACTATTACTATTACTATTATTATTGCCATCTCACTG  780
    I inquired with NCBI about a command for BLAST+ (neé StandALone BLAST) to have the aligment break at different increments or not at all. Like this:

    Code:
    Query  1     TTATTTTTCTTGATAGAATTAATTCTAATATTAGCACATTAAAAAATACTAAGTC-AAATTGTAATATTTCATTTGATATTGTATGCATACAATTTT-ATC---T--TACCTTTAAGAAT 113
                 ||||||| ||||||||  |||||| |||||||| |||||||||||||| |||||| ||||||||||||||||||||||  ||||||||||||||||| |||   |  ||||||||| |||
    Sbjct  542   TTATTTTGCTTGATAGCGTTAATTATAATATTACCACATTAAAAAATATTAAGTCAAAATTGTAATATTTCATTTGAT-CTGTATGCATACAATTTTAATCTTATCATACCTTTAATAAT  660
    They forwarded the request on to the development team, but don't have that functionality at the time in BLAST+. I was hoping someone might have had the same thought and wrote a little script to reformat these alignments?

    Thanks!
    Last edited by Genomics101; 12-04-2013, 04:42 PM.

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  • seqadmin
    Multiomics Techniques Advancing Disease Research
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