[Bioperl-l] Bioperl-l] frac_aligned_query returning results >1.

Thiago Venancio thiago.venancio at gmail.com
Fri Mar 2 06:38:48 EST 2007


Hi Sendu and Chris,

Thanks for the help.
As I mentioned, I have updated my SearchUtils file from:
http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/Search/SearchUtils.pm


I am also using the lates BioPerl version, installed from CPAN.

Please find a buggy blast report attached.
In this case, the frac_aligned_query() outputs "1.04", but I have others
with " 1.57" for example.

Just for a quantitative aspect, I got ">1" values in only 61 / 53,377.

The line where I call the function is :

print
$result->query_name."\t".$hit->frac_aligned_query()."\t".$hit->frac_identical(
'query' )."\n";

Thiago


-- 
"The way to get started is to quit talking and begin doing."
      Walt Disney

========================
Thiago Motta Venancio, MSc
PhD student in Bioinformatics
University of Sao Paulo
========================
-------------- next part --------------
BLASTN 2.2.6 [Apr-09-2003]


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= AEDES_02704.C
         (1069 letters)

Database: aaegypti.SCAFFOLDS-MASKED.AEDES1.fa
           4758 sequences; 1,383,971,543 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

supercontig:1:supercont1.157:1:2064756:1 supercontig supercont1.157   858   0.0

>supercontig:1:supercont1.157:1:2064756:1 supercontig supercont1.157
          Length = 2064756

 Score =  858 bits (433), Expect = 0.0
 Identities = 448/453 (98%)
 Strand = Plus / Plus


Query: 12     cattttaaatgcatatattgggtgccatcatgactgcctgactcctaaacttgacctcga 71
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759400 cattttaaatgcatatattgggtgccatcatgactgcctgactcctaaacttgacctcga 759459


Query: 72     ggcctatattctatcccttcttacatgtagtggcttaatcctagattgctggtactcacg 131
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759460 ggcctatattctatcccttcttacatgtagtggcttaatcctagattgctggtactcacg 759519


Query: 132    gcaccggctattatgctcccgccgcctctagctccaccagcctctgcatcctttctgacg 191
              |||||||| |||||||||||||||||| |||||||||||||||| |||||||||||||||
Sbjct: 759520 gcaccggccattatgctcccgccgcctttagctccaccagcctccgcatcctttctgacg 759579


Query: 192    gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccacctcagctgaagcggcta 251
              |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759580 gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccacctcagctgaagcggctg 759639


Query: 252    gctctcgacggtcattcaccgccgacgaccttgcactactgtgttgggaacccctggtcg 311
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759640 gctctcgacggtcattcaccgccgacgaccttgcactactgtgttgggaacccctggtcg 759699


Query: 312    tgagtcacagtccgctcttcctccgatgtgccaaatgtcaaacgctgatatggctacgga 371
              |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct: 759700 tgagtcacagtccgctcttcctccgatgtgtcaaatgtcaaacgctgatatggctacgga 759759


Query: 372    cgatcctccaccgcggtgttgggaacccctgagtgtagactcgctgggccttccttcgat 431
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759760 cgatcctccaccgcggtgttgggaacccctgagtgtagactcgctgggccttccttcgat 759819


Query: 432    gagccaaagaacgaaactgcaacgaaaaaaccc 464
              |||||||||||||||||||||||||||||||||
Sbjct: 759820 gagccaaagaacgaaactgcaacgaaaaaaccc 759852



 Score =  803 bits (405), Expect = 0.0
 Identities = 441/453 (97%)
 Strand = Plus / Plus


Query: 12     cattttaaatgcatatattgggtgccatcatgactgcctgactcctaaacttgacctcga 71
              ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct: 768455 cattttaaatgcatatattgggtgccatcatgactacctgactcctaaacttgacctcga 768514


Query: 72     ggcctatattctatcccttcttacatgtagtggcttaatcctagattgctggtactcacg 131
              ||||||||||||||| ||||||||||||||||||||||||||||||| ||||||||||||
Sbjct: 768515 ggcctatattctatctcttcttacatgtagtggcttaatcctagatttctggtactcacg 768574


Query: 132    gcaccggctattatgctcccgccgcctctagctccaccagcctctgcatcctttctgacg 191
              |||||||| |||||||||||||||||| |||||||||||||||| |||| ||||||||||
Sbjct: 768575 gcaccggccattatgctcccgccgcctttagctccaccagcctccgcattctttctgacg 768634


Query: 192    gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccacctcagctgaagcggcta 251
              ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Sbjct: 768635 gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccccctcagctgaagcggctg 768694


Query: 252    gctctcgacggtcattcaccgccgacgaccttgcactactgtgttgggaacccctggtcg 311
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 768695 gctctcgacggtcattcaccgccgacgaccttgcactactgtgttgggaacccctggtcg 768754


Query: 312    tgagtcacagtccgctcttcctccgatgtgccaaatgtcaaacgctgatatggctacgga 371
              |||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||
Sbjct: 768755 tgagtcacagtccgctcttcctccgatgtgccaaatgtcaactgctgatatggctacgga 768814


Query: 372    cgatcctccaccgcggtgttgggaacccctgagtgtagactcgctgggccttccttcgat 431
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 768815 cgatcctccaccgcggtgttgggaacccctgagtgtagactcgctgggccttccttcgat 768874


Query: 432    gagccaaagaacgaaactgcaacgaaaaaaccc 464
              |||||||||||| ||||||||||||||||||||
Sbjct: 768875 gagccaaagaacaaaactgcaacgaaaaaaccc 768907



 Score =  317 bits (160), Expect = 3e-84
 Identities = 170/172 (98%), Gaps = 1/172 (0%)
 Strand = Plus / Plus


Query: 899    ttcctttcaccgtatggccacgtgacgatgatgagctctggcgcctttcgcgtccggatg 958
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 769407 ttcctttcaccgtatggccacgtgacgatgatgagctctggcgcctttcgcgtccggatg 769466


Query: 959    ttttccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttt 1018
              |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 769467 ttttccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttc 769526


Query: 1019   tctttcgccggcttt-aacggcactaactttttgtggcaaaatccgcttatt 1069
              ||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 769527 tctttcgccggctttaaacggcactaactttttgtggcaaaatccgcttatt 769578



 Score =  311 bits (157), Expect = 2e-82
 Identities = 167/169 (98%), Gaps = 1/169 (0%)
 Strand = Plus / Plus


Query: 902    ctttcaccgtatggccacgtgacgatgatgagctctggcgcctttcgcgtccggatgttt 961
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 760355 ctttcaccgtatggccacgtgacgatgatgagctctggcgcctttcgcgtccggatgttt 760414


Query: 962    tccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttttct 1021
              |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct: 760415 tccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttctct 760474


Query: 1022   ttcgccggcttt-aacggcactaactttttgtggcaaaatccgcttatt 1069
              |||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 760475 ttcgccggctttaaacggcactaactttttgtggcaaaatccgcttatt 760523



 Score =  293 bits (148), Expect = 5e-77
 Identities = 151/152 (99%)
 Strand = Plus / Plus


Query: 587    ccccctttctttccgtcggaatcacgatccgagcagtagcgtcagcagacaatggatttg 646
              ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 769138 ccccctttctttccgtcggaatcgcgatccgagcagtagcgtcagcagacaatggatttg 769197


Query: 647    cggcgttcttattgttgaacaatgcgtgcccgtcctgatgccagcgatgatctcgtgatc 706
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 769198 cggcgttcttattgttgaacaatgcgtgcccgtcctgatgccagcgatgatctcgtgatc 769257


Query: 707    ggacaatcacgtcggtttcgaagcggttggcc 738
              ||||||||||||||||||||||||||||||||
Sbjct: 769258 ggacaatcacgtcggtttcgaagcggttggcc 769289



 Score =  293 bits (148), Expect = 5e-77
 Identities = 151/152 (99%)
 Strand = Plus / Plus


Query: 587    ccccctttctttccgtcggaatcacgatccgagcagtagcgtcagcagacaatggatttg 646
              ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 760083 ccccctttctttccgtcggaatcgcgatccgagcagtagcgtcagcagacaatggatttg 760142


Query: 647    cggcgttcttattgttgaacaatgcgtgcccgtcctgatgccagcgatgatctcgtgatc 706
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 760143 cggcgttcttattgttgaacaatgcgtgcccgtcctgatgccagcgatgatctcgtgatc 760202


Query: 707    ggacaatcacgtcggtttcgaagcggttggcc 738
              ||||||||||||||||||||||||||||||||
Sbjct: 760203 ggacaatcacgtcggtttcgaagcggttggcc 760234



 Score =  242 bits (122), Expect = 2e-61
 Identities = 125/126 (99%)
 Strand = Plus / Plus


Query: 463    cccaataaggggtttctcgtcgtgtgtgggtgcttcgagggaagcgacagtcaacctggc 522
              |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct: 768959 cccaataaggggtttctcgtcgtgtgtgggtgcttcgagggaagcgacagccaacctggc 769018


Query: 523    tcgcttcgaggtcctcctacggctcttgcagtggctatgcgctattggtggatgcaaaat 582
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 769019 tcgcttcgaggtcctcctacggctcttgcagtggctatgcgctattggtggatgcaaaat 769078


Query: 583    cgtccc 588
              ||||||
Sbjct: 769079 cgtccc 769084



 Score =  242 bits (122), Expect = 2e-61
 Identities = 125/126 (99%)
 Strand = Plus / Plus


Query: 463    cccaataaggggtttctcgtcgtgtgtgggtgcttcgagggaagcgacagtcaacctggc 522
              |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct: 759904 cccaataaggggtttctcgtcgtgtgtgggtgcttcgagggaagcgacagccaacctggc 759963


Query: 523    tcgcttcgaggtcctcctacggctcttgcagtggctatgcgctattggtggatgcaaaat 582
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759964 tcgcttcgaggtcctcctacggctcttgcagtggctatgcgctattggtggatgcaaaat 760023


Query: 583    cgtccc 588
              ||||||
Sbjct: 760024 cgtccc 760029



 Score =  123 bits (62), Expect = 1e-25
 Identities = 65/66 (98%)
 Strand = Plus / Plus


Query: 737    ccactctaaaatgcttcttcgtgccttctaggtcgtcgatatttgccgcgaaaaccgtga 796
              |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct: 769344 ccactctaaaatgcttcttcgtgccttctaggtcgttgatatttgccgcgaaaaccgtga 769403


Query: 797    tccttc 802
              ||||||
Sbjct: 769404 tccttc 769409



 Score =  121 bits (61), Expect = 4e-25
 Identities = 64/65 (98%)
 Strand = Plus / Plus


Query: 737    ccactctaaaatgcttcttcgtgccttctaggtcgtcgatatttgccgcgaaaaccgtga 796
              |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct: 760289 ccactctaaaatgcttcttcgtgccttctaggtcgttgatatttgccgcgaaaaccgtga 760348


Query: 797    tcctt 801
              |||||
Sbjct: 760349 tcctt 760353



 Score =  105 bits (53), Expect = 2e-20
 Identities = 68/73 (93%)


Query: 806     gttaaaaataatgaagattacacgtcatctaaactccatttatgcgatgtaaacatgacg 865
               ||||||||||||||||||||||| |||| |||||| ||||||||| ||| ||||||||||
Sbjct: 1251522 gttaaaaataatgaagattacacatcatgtaaacttcatttatgcaatgcaaacatgacg 1251463


Query: 866     tcatgtaaattta 878
               |||||||||||||
Sbjct: 1251462 tcatgtaaattta 1251450



 Score = 97.6 bits (49), Expect = 6e-18
 Identities = 70/77 (90%)
 Strand = Plus / Plus


Query: 802     cacagttaaaaataatgaagattacacgtcatctaaactccatttatgcgatgtaaacat 861
               ||||||||||| |||||||||||| |||| |||||||||  || ||||||||||||||||
Sbjct: 1251086 cacagttaaaactaatgaagattaaacgttatctaaactttatatatgcgatgtaaacat 1251145


Query: 862     gacgtcatgtaaattta 878
               || ||||||||||||||
Sbjct: 1251146 gaagtcatgtaaattta 1251162



 Score = 61.9 bits (31), Expect = 3e-07
 Identities = 37/39 (94%)
 Strand = Plus / Minus


Query: 802     cacagttaaaaataatgaagattacacgtcatctaaact 840
               |||||| ||||||||||||||||||||||||| ||||||
Sbjct: 1601368 cacagtaaaaaataatgaagattacacgtcatgtaaact 1601330



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