[Bioperl-l] Bioperl-l] frac_aligned_query returning results >1.
Thiago Venancio
thiago.venancio at gmail.com
Fri Mar 2 11:38:48 UTC 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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