[Bioperl-l] HOWTO:Graphics/BLAST output

N downloadondemand at gmail.com
Thu Aug 14 19:06:04 EDT 2008


Hello again!
Followed HOWTO:Graphics and encountered problem.
While parsing blast output i have clearly offending for me part of file. The
problem is that in this hit there are two HSPs, but the second one is in
"not right" strand orientation (Plus/Plus vs. Plus/Minus). How can i tell
bioperl to use only HSPs oriented along with the best-scored HSP? Or better,
althrough not related to this mailing list: How can i tell BLAST to put this
second HSP to a separate hit? What am i doing/thinking wrong?
Attached small png with problem. The second HSP is in white, but it is
biologically without sense, isn't it?
Thanks.




BLASTN 2.2.18 [Mar-02-2008]


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= gi|145226209
         (471 letters)

Database: ../database/1000
           24 sequences; 19,482 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits)
Value

gi|145226176 hypothetical_protein                                     599
e-174
gi|145226174 hypothetical_protein                                      30
0.007
gi|145226175 ATP-dependent_exoDNAse_(exonuclease_V)_alpha_subuni...    26
0.11
gi|145226190 hypothetical_protein                                      24
0.43
gi|145226195 protein_of_unknown_function_DUF1526                       22
1.7
gi|145226193 hypothetical_protein                                      22
1.7
gi|145226187 aminoglycoside_nucleotidyltransferase                     22
1.7
gi|145226181 diguanylate_cyclase                                       22
1.7
gi|145226179 hypothetical_protein                                      22
1.7
gi|145226178 hypothetical_protein                                      22
1.7
gi|145226177 putative_methyl-accepting_chemotaxis_sensory_transd...    22
1.7

>gi|145226176 hypothetical_protein
          Length = 477

 Score =  599 bits (302), Expect = e-174
 Identities = 428/470 (91%)
 Strand = Plus / Plus


Query: 1   atgaatgcagacgtgtcagtcaaccagtggaatccgttagaggtagccgctgaggcgaca 60
           |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||
Sbjct: 1   atgaatgcggacgtgtcagtcaaccagtggaatccgttagaggtggccgctgaggcgaca 60


Query: 61  atcgctgccgccacagccgcgctggtgtgggaaggcccagacagctacggggtgctggaa 120
           || ||||||||||| |||||  |||||||||||||||||||||||||||||||| ||||
Sbjct: 61  attgctgccgccacggccgcattggtgtgggaaggcccagacagctacggggtgttggag 120


Query: 121 cgggtcgccggggccacagcgaaaggcatagcaacagctcggatagccgccgaaatcatg 180
           ||||| ||||||||||||||||||||||| ||||||||||||||| ||||||||||||||
Sbjct: 121 cgggtagccggggccacagcgaaaggcatggcaacagctcggataaccgccgaaatcatg 180


Query: 181 gctgacgtcaccacctcagttcagttcactgcggccaccgaacatgcgcgcggcggcgct 240
           ||||||||||||||||||||||||||||||||||||  |||| |||||||||||||||||
Sbjct: 181 gctgacgtcaccacctcagttcagttcactgcggccgacgaagatgcgcgcggcggcgct 240


Query: 241 gtagcgggacttccggggtggctggcgccgcggtgggcggcgtccgtgcgtgccgcactg 300
           |||||||| ||||||||||||||||||||||||||||||||||||||||| | |||||||
Sbjct: 241 gtagcggggcttccggggtggctggcgccgcggtgggcggcgtccgtgcgcggcgcactg 300


Query: 301 gacgaactcgaagccgccgggcggcccggctacgccatggtcaaggcgatcacctggcct 360
           ||||| ||||||||||||||||| |||||| ||  |||| | || ||    ||  ||||
Sbjct: 301 gacgagctcgaagccgccgggcgccccggcgacatcatgatgaaagcccggacacggccg 360


Query: 361 gccttgcgcagcgtcgcggggtggacccaagacgggccgctgcaaacatggcagacggct 420
           ||  |||||||||| |||| ||||||||||||||| |||||||| |||||||||||||||
Sbjct: 361 gcactgcgcagcgtggcggtgtggacccaagacggaccgctgcagacatggcagacggct 420


Query: 421 ctaattgtgagcgaagcacggactgctctggctcaccgcgtaggcgtctg 470
           || || |||  |||||||||||||||||||||||||||||||||||||||
Sbjct: 421 ctgatcgtggacgaagcacggactgctctggctcaccgcgtaggcgtctg 470



 Score = 22.3 bits (11), Expect = 1.7
 Identities = 11/11 (100%)
 Strand = Plus / Minus


Query: 124 gtcgccggggc 134
           |||||||||||
Sbjct: 333 gtcgccggggc 323




The rest of output truncated...
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