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/
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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.
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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
Code:Query 1 TTATTTTTCTTGATAGAATTAATTCTAATATTAGCACATTAAAAAATACTAAGTC-AAATTGTAATATTTCATTTGATATTGTATGCATACAATTTT-ATC---T--TACCTTTAAGAAT 113 ||||||| |||||||| |||||| |||||||| |||||||||||||| |||||| |||||||||||||||||||||| ||||||||||||||||| ||| | ||||||||| ||| Sbjct 542 TTATTTTGCTTGATAGCGTTAATTATAATATTACCACATTAAAAAATATTAAGTCAAAATTGTAATATTTCATTTGAT-CTGTATGCATACAATTTTAATCTTATCATACCTTTAATAAT 660
Thanks!Last edited by Genomics101; 12-04-2013, 04:42 PM.
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