Entering edit mode
6.5 years ago
Ric
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430
HI, I ran blastn with blastall and I just wondering how could I extract each chromosome alignment to a separate file i.e. I have 10 chromosomes and I would like to get 10 files?
Here is my blastn output file example:
BLASTN 2.2.22 [Sep-27-2009]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= tig00022194
(464,128 letters)
Database: musa_acuminata_v2_pseudochromosome-1-11.fasta.clean
11 sequences; 397,008,016 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
chr08 8.185e+04 0.0
chr05 1.171e+04 0.0
chr11 1.080e+04 0.0
chr02 1.077e+04 0.0
chr09 1.037e+04 0.0
chr03 1.028e+04 0.0
chr07 1.002e+04 0.0
chr06 9932 0.0
chr10 9874 0.0
chr01 9846 0.0
chr04 9787 0.0
>chr08
Length = 44889171
Score = 8.185e+04 bits (41289), Expect = 0.0
Identities = 41909/42103 (99%), Gaps = 57/42103 (0%)
Strand = Plus / Minus
Query: 376639 ctctccctctccacctcagagcaggcctggagttttgaggagcgtcgtcgcaaccctgct 376698
|||| |||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct: 21232377 ctcttcctctccacctcagagcaggcctggagttt-gaggagcgtcgtcgcaaccctgct 21232319
Query: 376699 gtgtggatcattgctagagaggaggacgcttgacctccttcaccttctcctaaggatctg 376758
||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21232318 gtgtggatcatcgctagagaggaggacgcttgacctccttcaccttctcctaaggatctg 21232259
Query: 376759 caaggaaacagggatatacgatctccctaggtaacacaatatactctatacgcagttttg 376818
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21232258 caaggaaacagggatatacgatctccctaggtaacacaatatactctatacgcagttttg 21232199
Thank you in advance