scbi_blast 0.0.30

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Files changed (22) hide show
  1. data/History.txt +4 -0
  2. data/Manifest.txt +21 -0
  3. data/PostInstall.txt +7 -0
  4. data/README.rdoc +48 -0
  5. data/Rakefile +26 -0
  6. data/lib/scbi_blast.rb +15 -0
  7. data/lib/scbi_blast/batch_blast.rb +115 -0
  8. data/lib/scbi_blast/blast_hit.rb +115 -0
  9. data/lib/scbi_blast/blast_query.rb +37 -0
  10. data/lib/scbi_blast/blast_simplexml_result.rb +158 -0
  11. data/lib/scbi_blast/blast_table_result.rb +190 -0
  12. data/lib/scbi_blast/blast_xml_result.rb +152 -0
  13. data/lib/scbi_blast/dust_masker.rb +103 -0
  14. data/script/console +10 -0
  15. data/script/destroy +14 -0
  16. data/script/generate +14 -0
  17. data/test/blast.txt +252 -0
  18. data/test/blast.xml +173 -0
  19. data/test/empty_blast.xml +42 -0
  20. data/test/test_helper.rb +4 -0
  21. data/test/test_scbi_blast.rb +178 -0
  22. metadata +89 -0
data/script/destroy ADDED
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+ #!/usr/bin/env ruby
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+ APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
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+
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+ begin
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+ require 'rubigen'
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+ rescue LoadError
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+ require 'rubygems'
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+ require 'rubigen'
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+ end
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+ require 'rubigen/scripts/destroy'
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+
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+ ARGV.shift if ['--help', '-h'].include?(ARGV[0])
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+ RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
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+ RubiGen::Scripts::Destroy.new.run(ARGV)
data/script/generate ADDED
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+ #!/usr/bin/env ruby
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+ APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
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+
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+ begin
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+ require 'rubigen'
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+ rescue LoadError
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+ require 'rubygems'
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+ require 'rubigen'
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+ end
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+ require 'rubigen/scripts/generate'
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+
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+ ARGV.shift if ['--help', '-h'].include?(ARGV[0])
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+ RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
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+ RubiGen::Scripts::Generate.new.run(ARGV)
data/test/blast.txt ADDED
@@ -0,0 +1,252 @@
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+ BLASTN 2.2.20 [Feb-08-2009]
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+
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+
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+ Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
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+ Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
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+ "Gapped BLAST and PSI-BLAST: a new generation of protein database search
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+ programs", Nucleic Acids Res. 25:3389-3402.
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+
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+ Query= SEQ1_AA177160 ESTrp100 cDNA library from pre-meiotic male cones
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+ Pinus radiata cDNA 5'similar to FLORICAULA/LEAFY-like, mRNA sequence.
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+ (345 letters)
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+
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+ Database: db1.fasta
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+ 368,718 sequences; 223,306,471 total letters
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+
16
+ Searching..................................................done
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+
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+
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+
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+ Score E
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+ Sequences producing significant alignments: (bits) Value
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+
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+ AA177161 ESTrp101 cDNA library from pre-meiotic male cones Pinus... 684 0.0
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+ AA177160 ESTrp100 cDNA library from pre-meiotic male cones Pinus... 684 0.0
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+ AA177162 ESTrp102 cDNA library from pre-meiotic male cones Pinus... 678 0.0
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+ CT583549 Pinus pinaster bud EST. 597 e-169
27
+ DT633465 EST1148396 Normalized pine embryo library, Lib_D Pinus ... 34 3.6
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+ DR692334 EST1082422 Normalized pine embryo library, Lib_D Pinus ... 34 3.6
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+ DR180575 RTMNUT1_33_B08.g1_A029 Roots minus micronutrients Pinus... 34 3.6
30
+ DR116741 RTMG1_2_B05.g1_A029 Roots minus magnesium Pinus taeda c... 34 3.6
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+ DR069728 RTDK1_9_C06.b1_A029 Roots, dark Pinus taeda cDNA clone ... 34 3.6
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+ DR069474 RTDK1_7_B01.g1_A029 Roots, dark Pinus taeda cDNA clone ... 34 3.6
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+ CX649059 COLD1_32_E05.g1_A029 Root cold Pinus taeda cDNA clone C... 34 3.6
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+ CX646190 COLD1_7_G09.g1_A029 Root cold Pinus taeda cDNA clone CO... 34 3.6
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+ CT574774 Pinus pinaster bud EST. 34 3.6
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+ CO170771 NDL1_16_F10.g1_A029 Needles control Pinus taeda cDNA cl... 34 3.6
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+ CF475661 RTWW2_11_H07.g1_A021 Well-watered loblolly pine roots W... 34 3.6
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+ CD026097 NXSI_097_B06_F NXSI (Nsf Xylem Side wood Inclined) Pinu... 34 3.6
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+ BG039660 NXSI_102_F04_F NXSI (Nsf Xylem Side wood Inclined) Pinu... 34 3.6
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+ BE123617 NXNV_146_E10_F Nsf Xylem Normal wood Vertical Pinus tae... 34 3.6
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+
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+ >AA177161 ESTrp101 cDNA library from pre-meiotic male cones Pinus
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+ radiata cDNA 5'similar to FLORICAULA/LEAFY-like, mRNA
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+ sequence.
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+ Length = 450
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+
47
+ Score = 684 bits (345), Expect = 0.0
48
+ Identities = 345/345 (100%)
49
+ Strand = Plus / Plus
50
+
51
+
52
+ Query: 1 gaaagcttttctgcagctttcttcaagtgggaccagagaccgcctgctcttgcgccccca 60
53
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 87 gaaagcttttctgcagctttcttcaagtgggaccagagaccgcctgctcttgcgccccca 146
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+
56
+
57
+ Query: 61 caaatgcagaggagtgcaggattggaagctcagcgtattttccatgacttcggtgttcca 120
58
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 147 caaatgcagaggagtgcaggattggaagctcagcgtattttccatgacttcggtgttcca 206
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+
61
+
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+ Query: 121 aatgcagctgccatggcagcttccaataacagcagcagttgcaggaaggaattgaactgc 180
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 207 aatgcagctgccatggcagcttccaataacagcagcagttgcaggaaggaattgaactgc 266
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+
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+
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+ Query: 181 ctggaggagctcttcaggaattacggcgtgagatacataacgctgaccaaaatggtggac 240
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 267 ctggaggagctcttcaggaattacggcgtgagatacataacgctgaccaaaatggtggac 326
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+
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+
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+ Query: 241 atggggttcactgtgaacacattggttaatatgactgaacaagagctggatgatctagtc 300
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 327 atggggttcactgtgaacacattggttaatatgactgaacaagagctggatgatctagtc 386
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+
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+
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+ Query: 301 aggacccttgttgagatataccgtgttgagctcctggttggggag 345
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+ |||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 387 aggacccttgttgagatataccgtgttgagctcctggttggggag 431
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+
81
+
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+ >AA177160 ESTrp100 cDNA library from pre-meiotic male cones Pinus
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+ radiata cDNA 5'similar to FLORICAULA/LEAFY-like, mRNA
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+ sequence.
85
+ Length = 449
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+
87
+ Score = 684 bits (345), Expect = 0.0
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+ Identities = 345/345 (100%)
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+ Strand = Plus / Plus
90
+
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+
92
+ Query: 1 gaaagcttttctgcagctttcttcaagtgggaccagagaccgcctgctcttgcgccccca 60
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 86 gaaagcttttctgcagctttcttcaagtgggaccagagaccgcctgctcttgcgccccca 145
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+
96
+
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+ Query: 61 caaatgcagaggagtgcaggattggaagctcagcgtattttccatgacttcggtgttcca 120
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 146 caaatgcagaggagtgcaggattggaagctcagcgtattttccatgacttcggtgttcca 205
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+
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+
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+ Query: 121 aatgcagctgccatggcagcttccaataacagcagcagttgcaggaaggaattgaactgc 180
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 206 aatgcagctgccatggcagcttccaataacagcagcagttgcaggaaggaattgaactgc 265
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+
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+
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+ Query: 181 ctggaggagctcttcaggaattacggcgtgagatacataacgctgaccaaaatggtggac 240
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 266 ctggaggagctcttcaggaattacggcgtgagatacataacgctgaccaaaatggtggac 325
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+
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+
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+ Query: 241 atggggttcactgtgaacacattggttaatatgactgaacaagagctggatgatctagtc 300
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+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 326 atggggttcactgtgaacacattggttaatatgactgaacaagagctggatgatctagtc 385
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+
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+
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+ Query: 301 aggacccttgttgagatataccgtgttgagctcctggttggggag 345
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+ |||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 386 aggacccttgttgagatataccgtgttgagctcctggttggggag 430
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+
121
+
122
+ BLASTN 2.2.20 [Feb-08-2009]
123
+
124
+
125
+ Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
126
+ Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
127
+ "Gapped BLAST and PSI-BLAST: a new generation of protein database search
128
+ programs", Nucleic Acids Res. 25:3389-3402.
129
+
130
+ Query= SEQ7_AA216455 ESTH3 Pinus radiata somatic embryogenic library
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+ Pinus radiata cDNA clonepPRE22B 5' similar to Hypothetical translation
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+ elongation factor, mRNAsequence.
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+ (325 letters)
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+
135
+ Database: db1.fasta
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+ 368,718 sequences; 223,306,471 total letters
137
+
138
+ Searching..................................................done
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+
140
+
141
+
142
+ Score E
143
+ Sequences producing significant alignments: (bits) Value
144
+
145
+ AA216455 ESTH3 Pinus radiata somatic embryogenic library Pinus r... 597 e-169
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+ CO171201 NDL1_19_G07.g1_A029 Needles control Pinus taeda cDNA cl... 490 e-137
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+ FE522525 li0678875 Radiata pine mature latewood cDNA library Pin... 486 e-136
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+ DR079374 RTFEPL1_10_H01.g1_A029 Roots plus added iron Pinus taed... 474 e-132
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+ DT639026 EST1153957 Normalized pine embryo library, Lib_D Pinus ... 470 e-131
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+ DT631905 EST1146836 Normalized pine embryo library, Lib_D Pinus ... 470 e-131
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+ DR695137 EST1085230 Normalized pine embryo library, Lib_D Pinus ... 470 e-131
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+ CO169296 NDL1_6_B10.b1_A029 Needles control Pinus taeda cDNA clo... 470 e-131
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+ DR060251 RTNIT1_26_E02.g1_A029 Roots minus nitrogen Pinus taeda ... 464 e-129
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+ BG039539 NXSI_100_B09_F NXSI (Nsf Xylem Side wood Inclined) Pinu... 452 e-126
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+ BX255307 Pinus pinaster xylem EST, clone PP004C03 similar to ELO... 442 e-123
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+ BX252919 Pinus pinaster xylem EST, clone PP074H07 similar to ELO... 436 e-121
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+ CT575805 Pinus pinaster bud EST. 418 e-116
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+ DR098748 STRR1_47_D06.g1_A033 Stem Response Resistant Pinus taed... 381 e-104
159
+ BX677971 Pinus pinaster root EST, clone RN47E06 373 e-102
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+ DR690449 EST1080535 Normalized pine embryo library, Lib_D Pinus ... 343 3e-93
161
+ DR683892 EST1073968 Normalized pine embryo library, Lib_D Pinus ... 317 2e-85
162
+ CF477767 RTWW3_9_H07.g1_A022 Well-watered loblolly pine roots WW... 301 9e-81
163
+ CF395463 RTDS2_11_C10.g1_A021 Drought-stressed loblolly pine roo... 274 2e-72
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+ CT577300 Pinus pinaster bud EST. 254 2e-66
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+ CT579809 Pinus pinaster bud EST. 186 4e-46
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+ CT577738 Pinus pinaster bud EST. 186 4e-46
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+ BX675172 Pinus pinaster root EST, clone RN10D10 186 4e-46
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+ CO169359 NDL1_6_B10.g1_A029 Needles control Pinus taeda cDNA clo... 139 8e-32
169
+ FE522437 li0674425 Radiata pine mature latewood cDNA library Pin... 127 3e-28
170
+ BX677705 Pinus pinaster root EST, clone RN43D07 125 1e-27
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+ CD024054 NXRV_027_C03_F NXRV (Nsf Xylem Root wood Vertical) Pinu... 119 7e-26
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+ FG614563 FEGLCD006_01-B05-T7 PR_FC library Pinus rigida x Pinus ... 38 0.22
173
+
174
+ >AA216455 ESTH3 Pinus radiata somatic embryogenic library Pinus
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+ radiata cDNA clonepPRE22B 5' similar to Hypothetical
176
+ translation elongation factor, mRNAsequence.
177
+ Length = 381
178
+
179
+ Score = 597 bits (301), Expect = e-169
180
+ Identities = 325/325 (100%)
181
+ Strand = Plus / Plus
182
+
183
+
184
+ Query: 1 agaggcagaggccgagggtgcaagcgcagtagtaaatccttnctctgcatngaagagatc 60
185
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
186
+ Sbjct: 34 agaggcagaggccgagggtgcaagcgcagtagtaaatccttnctctgcatngaagagatc 93
187
+
188
+
189
+ Query: 61 aagaatggccgtctcattctccaatctcagaactgagtcaggcgtggagaagctggatca 120
190
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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+ Sbjct: 94 aagaatggccgtctcattctccaatctcagaactgagtcaggcgtggagaagctggatca 153
192
+
193
+
194
+ Query: 121 gctctcgctcacacgcagttatntttctgggtntcaggcatcaacggatgacataagagt 180
195
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
196
+ Sbjct: 154 gctctcgctcacacgcagttatntttctgggtntcaggcatcaacggatgacataagagt 213
197
+
198
+
199
+ Query: 181 atnctctgcacttggncangcacctggatcccattacatcaatgcctcccgttggtacaa 240
200
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
201
+ Sbjct: 214 atnctctgcacttggncangcacctggatcccattacatcaatgcctcccgttggtacaa 273
202
+
203
+
204
+ Query: 241 cacatctgtgccttactagccccaagttttctggggatggtgttggtgttcacatcgang 300
205
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
206
+ Sbjct: 274 cacatctgtgccttactagccccaagttttctggggatggtgttggtgttcacatcgang 333
207
+
208
+
209
+ Query: 301 gagggagtcagccatcaaaggacga 325
210
+ |||||||||||||||||||||||||
211
+ Sbjct: 334 gagggagtcagccatcaaaggacga 358
212
+
213
+
214
+ >CO171201 NDL1_19_G07.g1_A029 Needles control Pinus taeda cDNA clone
215
+ NDL1_19_G07_A0295', mRNA sequence.
216
+ Length = 771
217
+
218
+ Score = 490 bits (247), Expect = e-137
219
+ Identities = 298/315 (94%), Gaps = 2/315 (0%)
220
+ Strand = Plus / Plus
221
+
222
+
223
+ Query: 10 ggccgagggtgcaagcgcagtagtaaatccttnctctgcatngaagagatcaagaatggc 69
224
+ |||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||
225
+ Sbjct: 1 ggccgagggtgcaagcgcagtagtaaatcctttctctgcatagaagagatcaagaatggc 60
226
+
227
+
228
+ Query: 70 cgtctcattctccaatctcagaactgagtcaggcgtggagaagctggatcagctctcgct 129
229
+ ||||||||||||||||||||| |||||||||||||||||| ||||||||||| ||| |||
230
+ Sbjct: 61 cgtctcattctccaatctcagcactgagtcaggcgtggagcagctggatcagttcttgct 120
231
+
232
+
233
+ Query: 130 cacacgcagttatntttctgggtntcaggcatcaacggatgacataagagtatnctctgc 189
234
+ ||||||||||||| ||||||||| ||||||||||||||||||||||||||||| ||||||
235
+ Sbjct: 121 cacacgcagttatatttctgggtatcaggcatcaacggatgacataagagtatactctgc 180
236
+
237
+
238
+ Query: 190 acttggncangcacctggatcccattacatcaatgcctcccgttggtacaa-cacatctg 248
239
+ |||||| || ||||||||||||||||||||||||||||||||||||||||| ||||||||
240
+ Sbjct: 181 acttggccaagcacctggatcccattacatcaatgcctcccgttggtacaaccacatctg 240
241
+
242
+
243
+ Query: 249 tgccttactagccccaag-ttttctggggatggtgttggtgttcacatcganggagggag 307
244
+ |||||||||||||||||| ||||||||||| |||||||||||||| || || ||||||||
245
+ Sbjct: 241 tgccttactagccccaagtttttctggggaaggtgttggtgttcaaattgaaggagggag 300
246
+
247
+
248
+ Query: 308 tcagccatcaaagga 322
249
+ |||||||||||||||
250
+ Sbjct: 301 tcagccatcaaagga 315
251
+
252
+
data/test/blast.xml ADDED
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+ <?xml version="1.0"?>
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+ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
3
+ <BlastOutput>
4
+ <BlastOutput_program>blastn</BlastOutput_program>
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+ <BlastOutput_version>BLASTN 2.2.22+</BlastOutput_version>
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+ <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), &quot;A greedy algorithm for aligning DNA sequences&quot;, J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference>
7
+ <BlastOutput_db>../../DB/formatted/contaminants.fasta</BlastOutput_db>
8
+ <BlastOutput_query-ID>1</BlastOutput_query-ID>
9
+ <BlastOutput_query-def>GEM-10-C10</BlastOutput_query-def>
10
+ <BlastOutput_query-len>752</BlastOutput_query-len>
11
+ <BlastOutput_param>
12
+ <Parameters>
13
+ <Parameters_expect>10</Parameters_expect>
14
+ <Parameters_sc-match>1</Parameters_sc-match>
15
+ <Parameters_sc-mismatch>-2</Parameters_sc-mismatch>
16
+ <Parameters_gap-open>0</Parameters_gap-open>
17
+ <Parameters_gap-extend>0</Parameters_gap-extend>
18
+ <Parameters_filter>L;m;</Parameters_filter>
19
+ </Parameters>
20
+ </BlastOutput_param>
21
+ <BlastOutput_iterations>
22
+ <Iteration>
23
+ <Iteration_iter-num>1</Iteration_iter-num>
24
+ <Iteration_query-ID>1</Iteration_query-ID>
25
+ <Iteration_query-def>GEM-10-C10</Iteration_query-def>
26
+ <Iteration_query-len>752</Iteration_query-len>
27
+ <Iteration_hits>
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+ <Hit>
29
+ <Hit_num>1</Hit_num>
30
+ <Hit_id>gi|49175990|ref|NC_000913.2|</Hit_id>
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+ <Hit_def>Escherichia coli K12, complete genome</Hit_def>
32
+ <Hit_accession>NC_000913</Hit_accession>
33
+ <Hit_len>4639675</Hit_len>
34
+ <Hit_hsps>
35
+ <Hsp>
36
+ <Hsp_num>1</Hsp_num>
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+ <Hsp_bit-score>300.277537912453</Hsp_bit-score>
38
+ <Hsp_score>162</Hsp_score>
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+ <Hsp_evalue>1.75690828542385e-80</Hsp_evalue>
40
+ <Hsp_query-from>280</Hsp_query-from>
41
+ <Hsp_query-to>447</Hsp_query-to>
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+ <Hsp_hit-from>365520</Hsp_hit-from>
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+ <Hsp_hit-to>365352</Hsp_hit-to>
44
+ <Hsp_query-frame>1</Hsp_query-frame>
45
+ <Hsp_hit-frame>-1</Hsp_hit-frame>
46
+ <Hsp_identity>167</Hsp_identity>
47
+ <Hsp_positive>167</Hsp_positive>
48
+ <Hsp_gaps>1</Hsp_gaps>
49
+ <Hsp_align-len>169</Hsp_align-len>
50
+ <Hsp_qseq>ATTAC-AATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGC</Hsp_qseq>
51
+ <Hsp_hseq>ATTACGGATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGC</Hsp_hseq>
52
+ <Hsp_midline>||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
53
+ </Hsp>
54
+ </Hit_hsps>
55
+ </Hit>
56
+ <Hit>
57
+ <Hit_num>2</Hit_num>
58
+ <Hit_id>Escherichia</Hit_id>
59
+ <Hit_def>Escherichia coli str. K12 substr. DH10B DNA genomico</Hit_def>
60
+ <Hit_accession>Escherichia</Hit_accession>
61
+ <Hit_len>4686137</Hit_len>
62
+ <Hit_hsps>
63
+ <Hsp>
64
+ <Hsp_num>1</Hsp_num>
65
+ <Hsp_bit-score>98.992725807625</Hsp_bit-score>
66
+ <Hsp_score>53</Hsp_score>
67
+ <Hsp_evalue>6.87883996966399e-20</Hsp_evalue>
68
+ <Hsp_query-from>395</Hsp_query-from>
69
+ <Hsp_query-to>447</Hsp_query-to>
70
+ <Hsp_hit-from>1384940</Hsp_hit-from>
71
+ <Hsp_hit-to>1384888</Hsp_hit-to>
72
+ <Hsp_query-frame>1</Hsp_query-frame>
73
+ <Hsp_hit-frame>-1</Hsp_hit-frame>
74
+ <Hsp_identity>53</Hsp_identity>
75
+ <Hsp_positive>53</Hsp_positive>
76
+ <Hsp_gaps>0</Hsp_gaps>
77
+ <Hsp_align-len>53</Hsp_align-len>
78
+ <Hsp_qseq>GGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGC</Hsp_qseq>
79
+ <Hsp_hseq>GGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGC</Hsp_hseq>
80
+ <Hsp_midline>|||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
81
+ </Hsp>
82
+ </Hit_hsps>
83
+ </Hit>
84
+ </Iteration_hits>
85
+ <Iteration_stat>
86
+ <Statistics>
87
+ <Statistics_db-num>36</Statistics_db-num>
88
+ <Statistics_db-len>59671529</Statistics_db-len>
89
+ <Statistics_hsp-len>0</Statistics_hsp-len>
90
+ <Statistics_eff-space>43380547283</Statistics_eff-space>
91
+ <Statistics_kappa>0.46</Statistics_kappa>
92
+ <Statistics_lambda>1.28</Statistics_lambda>
93
+ <Statistics_entropy>0.85</Statistics_entropy>
94
+ </Statistics>
95
+ </Iteration_stat>
96
+ </Iteration>
97
+ <Iteration>
98
+ <Iteration_iter-num>2</Iteration_iter-num>
99
+ <Iteration_query-ID>2</Iteration_query-ID>
100
+ <Iteration_query-def>GEM-10bis-C10</Iteration_query-def>
101
+ <Iteration_query-len>754</Iteration_query-len>
102
+ <Iteration_hits>
103
+ <Hit>
104
+ <Hit_num>1</Hit_num>
105
+ <Hit_id>gi|49175990|ref|NC_000913.2|</Hit_id>
106
+ <Hit_def>Escherichia coli K12, complete genome</Hit_def>
107
+ <Hit_accession>NC_000913</Hit_accession>
108
+ <Hit_len>4639675</Hit_len>
109
+ <Hit_hsps>
110
+ <Hsp>
111
+ <Hsp_num>1</Hsp_num>
112
+ <Hsp_bit-score>300.277537912453</Hsp_bit-score>
113
+ <Hsp_score>162</Hsp_score>
114
+ <Hsp_evalue>1.76174159570011e-80</Hsp_evalue>
115
+ <Hsp_query-from>282</Hsp_query-from>
116
+ <Hsp_query-to>449</Hsp_query-to>
117
+ <Hsp_hit-from>365520</Hsp_hit-from>
118
+ <Hsp_hit-to>365352</Hsp_hit-to>
119
+ <Hsp_query-frame>1</Hsp_query-frame>
120
+ <Hsp_hit-frame>-1</Hsp_hit-frame>
121
+ <Hsp_identity>167</Hsp_identity>
122
+ <Hsp_positive>167</Hsp_positive>
123
+ <Hsp_gaps>1</Hsp_gaps>
124
+ <Hsp_align-len>169</Hsp_align-len>
125
+ <Hsp_qseq>ATTAC-AATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGC</Hsp_qseq>
126
+ <Hsp_hseq>ATTACGGATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGC</Hsp_hseq>
127
+ <Hsp_midline>||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
128
+ </Hsp>
129
+ </Hit_hsps>
130
+ </Hit>
131
+ <Hit>
132
+ <Hit_num>2</Hit_num>
133
+ <Hit_id>Escherichia</Hit_id>
134
+ <Hit_def>Escherichia coli str. K12 substr. DH10B DNA genomico</Hit_def>
135
+ <Hit_accession>Escherichia</Hit_accession>
136
+ <Hit_len>4686137</Hit_len>
137
+ <Hit_hsps>
138
+ <Hsp>
139
+ <Hsp_num>1</Hsp_num>
140
+ <Hsp_bit-score>98.992725807625</Hsp_bit-score>
141
+ <Hsp_score>53</Hsp_score>
142
+ <Hsp_evalue>6.89776387604546e-20</Hsp_evalue>
143
+ <Hsp_query-from>397</Hsp_query-from>
144
+ <Hsp_query-to>449</Hsp_query-to>
145
+ <Hsp_hit-from>1384940</Hsp_hit-from>
146
+ <Hsp_hit-to>1384888</Hsp_hit-to>
147
+ <Hsp_query-frame>1</Hsp_query-frame>
148
+ <Hsp_hit-frame>-1</Hsp_hit-frame>
149
+ <Hsp_identity>53</Hsp_identity>
150
+ <Hsp_positive>53</Hsp_positive>
151
+ <Hsp_gaps>0</Hsp_gaps>
152
+ <Hsp_align-len>53</Hsp_align-len>
153
+ <Hsp_qseq>GGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGC</Hsp_qseq>
154
+ <Hsp_hseq>GGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGC</Hsp_hseq>
155
+ <Hsp_midline>|||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
156
+ </Hsp>
157
+ </Hit_hsps>
158
+ </Hit>
159
+ </Iteration_hits>
160
+ <Iteration_stat>
161
+ <Statistics>
162
+ <Statistics_db-num>36</Statistics_db-num>
163
+ <Statistics_db-len>59671529</Statistics_db-len>
164
+ <Statistics_hsp-len>0</Statistics_hsp-len>
165
+ <Statistics_eff-space>43499888541</Statistics_eff-space>
166
+ <Statistics_kappa>0.46</Statistics_kappa>
167
+ <Statistics_lambda>1.28</Statistics_lambda>
168
+ <Statistics_entropy>0.85</Statistics_entropy>
169
+ </Statistics>
170
+ </Iteration_stat>
171
+ </Iteration>
172
+ </BlastOutput_iterations>
173
+ </BlastOutput>