dna_sequence_aligner 0.0.2

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Files changed (24) hide show
  1. data/.gitignore +8 -0
  2. data/History +10 -0
  3. data/LICENSE +22 -0
  4. data/README.rdoc +58 -0
  5. data/Rakefile +45 -0
  6. data/VERSION +1 -0
  7. data/bin/dna_sequence_aligner +61 -0
  8. data/bin/dna_translator.rb +59 -0
  9. data/lib/bio/alignment/dna_sequence.rb +313 -0
  10. data/older/align_all.rb +160 -0
  11. data/older/align_to_template.rb +143 -0
  12. data/reference/clustalw_opts.txt +73 -0
  13. data/script/fasta_compile_annotated.rb +19 -0
  14. data/spec/align_spec.rb +67 -0
  15. data/spec/spec_helper.rb +6 -0
  16. data/spec/testfiles/HA-mKSR1-KSRF1.txt +19 -0
  17. data/spec/testfiles/HA-mKSR1-KSRF2.txt +20 -0
  18. data/spec/testfiles/HA-mKSR1-KSRF3.txt +20 -0
  19. data/spec/testfiles/HA-mKSR1-KSRF4.txt +20 -0
  20. data/spec/testfiles/HA-mKSR1-KSRF5.txt +20 -0
  21. data/spec/testfiles/HA-mKSR1-OXL33.txt +20 -0
  22. data/spec/testfiles/KSR1_mouse_NM_013571_in_HA_pREX.ANNOTATED.fasta +77 -0
  23. data/spec/testfiles/testcase.fasta +55 -0
  24. metadata +99 -0
data/spec/spec_helper.rb ADDED
@@ -0,0 +1,6 @@
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+ require 'rubygems'
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+ require 'spec/more'
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+
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+ TESTFILES = File.expand_path(File.dirname(__FILE__) + '/testfiles')
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+
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+ Bacon.summary_on_exit
data/spec/testfiles/HA-mKSR1-KSRF1.txt ADDED
@@ -0,0 +1,19 @@
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+ >100122-36_G07_HA-mKSR1-KSRF1.ab1 950 [cut-JTP]
2
+ GNNNNNCCAGAGATGCTGCGGCGCTGGGGGGCCAGCACGGAGGAGTGCAG
3
+ CCGCCTACAGCAAGCCCTTACCTGCCTTCGGAAGGTGACTGGCCTGGGAG
4
+ GGGAGCACAAAATGGACTCAGGTTGGAGTTCAACAGATGCTCGAGACAGT
5
+ AGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCTGGGCAGAGCGGGTGC
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+ CAGCACTCAGGGACCCCGTTCCATCTCCGTGTCCGCCCTGCCTGCCTCAG
7
+ ACTCTCCGGTCCCCGGCCTCAGTGAGGGCCTCTCGGACTCCTGTATCCCC
8
+ TTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCTGCACAGCTTCATCAC
9
+ GCCCCCTACCACACCCCAGCTACGACGGCACGCCAAGCTGAAGCCACCAA
10
+ GGACACCCCCACCGCCAAGCCGCAAGGTCTTCCAGCTGCTCCCCAGCTTC
11
+ CCCACACTCACACGGAGCAAGTCCCACGAGTCCCAGCTGGGAAACCGAAT
12
+ CGACGACGTCACCCCGATGAAGTTTGAACTCCCTCATGGATCCCCACAGC
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+ TGGTACGAAGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAG
14
+ TCATGGTTGTCACAGGTGTGCAACGTGTGCCAGAAGAGCATGATTTTTGG
15
+ CGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAAGG
16
+ AAGCTCCCGCCTGCAGGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGG
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+ ACAGAGTCTGTCCCGTCAGATATCAACAACCCAGTGGACAGAGCAGCAGA
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+ GCCCCATTTTGGAACCCTTCCCAAGGCCCTGACAAAGAAGGAGCACCCTC
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+ CAGCCATGAACCTGGACTCCAGCAGCAACCCATCCTCC
data/spec/testfiles/HA-mKSR1-KSRF2.txt ADDED
@@ -0,0 +1,20 @@
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+ >100122-36_I07_HA-mKSR1-KSRF2.ab1 950
2
+ NNTNANCGCANGTCTTCCAGCTGCTCCCCAGCTTCCCCACACTCACACGG
3
+ AGCAAGTCCCACGAGTCCCAGCTGGGAAACCGAATCGACGACGTCACCCC
4
+ GATGAAGTTTGAACTCCCTCATGGATCCCCACAGCTGGTACGAAGGGATA
5
+ TCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAG
6
+ GTGTGCAACGTGTGCCAGAAGAGCATGATTTTTGGCGTGAAGTGCAAACA
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+ CTGCAGGTTAAAATGCCATAACAAGTGCACAAAGGAAGCTCCCGCCTGCA
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+ GGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGGACAGAGTCTGTCCCG
9
+ TCAGATATCAACAACCCAGTGGACAGAGCAGCAGAGCCCCATTTTGGAAC
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+ CCTTCCCAAGGCCCTGACAAAGAAGGAGCACCCTCCAGCCATGAACCTGG
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+ ACTCCAGCAGCAACCCATCCTCCACCACGTCCTCCACACCCTCATCGCCG
12
+ GCACCTTTCCTGACCTCATCTAATCCCTCCAGTGCCACCACGCCTCCCAA
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+ CCCGTCACCTGGCCAGCGGGACAGCAGGTTCAGCTTCCCAGACATTTCAG
14
+ CCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAGCCGACAGTACACGGCTC
15
+ GACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAGGCTGA
16
+ GGAGCCTGAGGCTGGCAAGTCAGAGGCAGAGGATGACGAGGAGGATGAGG
17
+ TGGACGACCTCCCCAGCTCCCGCCGGCCCTGGAGGGGCCCCATCTCTCGA
18
+ AAGGCCAGCCAGACCAGCGTTTACCTGCAAGAGTGGGACATCCCCTTTGA
19
+ ACAGGTGGAACTGGGCGAGCCCATTGGACAGGGTCGCTGGGGCCGGGTGC
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+ ACCGAGCCGTTGGCATGGCGAGGTGGNATTCGGCTGCTGGAGATGGANGN
data/spec/testfiles/HA-mKSR1-KSRF3.txt ADDED
@@ -0,0 +1,20 @@
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+ >100122-36_K07_HA-mKSR1-KSRF3.ab1 950
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+ NNNNNAGNCTGGGCANTCAGAGGCAGAGGANGACGAGGAGGATGAGGTGG
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+ ACGACCTCCCCAGCTCCCGCCGGCCCTGGAGGGGCCCCATCTCTCGAAAG
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+ GCCAGCCAGACCAGCGTTTACCTGCAAGAGTGGGACATCCCCTTTGAACA
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+ GGTGGAACTGGGCGAGCCCATTGGACAGGGTCGCTGGGGCCGGGTGCACC
6
+ GAGGCCGTTGGCATGGCGAGGTGGCCATTCGGCTGCTGGAGATGGACGGC
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+ CACAATCAGGACCACCTGAAGCTGTTCAAGAAAGAGGTGATGAACTACCG
8
+ GCAGACGCGGCATGAGAACGTGGTGCTCTTCATGGGGGCCTGCATGAACC
9
+ CACCTCACCTGGCCATTATCACCAGCTTCTGCAAGGGGCGGACATTGCAT
10
+ TCATTCGTGAGGGACCCCAAGACGTCTCTGGACATCAATAAGACTAGGCA
11
+ GATCGCCCAGGAGATCATCAAGGGCATGGGTTATCTTCATGCAAAAGGCA
12
+ TCGTGCACAAGGACCTCAAGTCCAAGAATGTCTTCTATGACAACGGCAAA
13
+ GTGGTCATCACAGACTTCGGGCTGTTTGGGATCTCGGGTGTGGTCCGAGA
14
+ GGAACGGCGCGAGAACCAACTGAAACTGTCACATGACTGGCTGTGCTACC
15
+ TGGCCCCCGAGATCGTACGAGAAATGATCCCAGGGCGGGACGAGGACCAG
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+ CTGCCCTTCTCCAAAGCAGCCGATGTCTATGCATTCGGGACTGTGTGGTA
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+ TGAACTACAGGCAAGAGACTGGCCCTTTAAGCACCAGCCTGCTGAGGCCT
18
+ TGATCTGGCAGATTGGAAGTGGGGAAGGAGTACGGCGCGTCCTGCATCCG
19
+ TCAGCCTGGGGAAGGAGTCGGCGAGATCCTGTCTGCCTGCTGGGCTTTCG
20
+ ATCTGCAGGAGAGACCCAGCTTCAGCCTGCTGATGGACATGCTGGAGAAG
data/spec/testfiles/HA-mKSR1-KSRF4.txt ADDED
@@ -0,0 +1,20 @@
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+ >100122-36_M07_HA-mKSR1-KSRF4.ab1 950
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+ CNNNNNAAANAAANTTGTTCCGGGGGGGGGAGGAGAANGGCTCCCTTTCT
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+ CAAACCACCAAATTTTTATGCTTTGGGGAGGGGGGGGAAAAAACAACGGG
4
+ AAAAAGAGGGCCTTTTAAACCCCCCCCCTGGTGAGGTTTTTTTGGGAAAA
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+ ATGGAAGGGGGGGAGGGAGTGGGGCGCGCCCTGCCCCCCGTCCGCGGGGG
6
+ AAAGGAAGGGGGAAAGTTCTTGTGTGCGGGGGGGTTTTTCTTTCGGGAGA
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+ AAACCCCCTCTTCCCCCCTGTTGAGGAACTTGGGGAAGGGGCTCCCAAAG
8
+ CTGACCGGGCGCTTCCCCCCCCGGGGGCTTTTTGGAAGGTGGGCTAATTT
9
+ AAACACCAAAAAATTCTCCCCCCTTTTAAAAGGGTTGGCCGGGGGCCCCG
10
+ GGGACCCGGGAAACCAAAAATTGTGGGGCGCCCCCCACCAGGGGGCCCGG
11
+ GGTTTCGGGGGGGGCAATTTCCCCCCCTCCCCCCCCAACCCCTCCCCGCC
12
+ CGTTTTAATAATTTTGGGGGAAAACCCCGTTAGAAATAGGGCGGGGGTGT
13
+ TTTTTTTTTTTTTTTTTTTCCCCCCATTTGGCCTTTTTGGGAAAGGGGGG
14
+ GGGCCGGAAAACGGGCCCTTTTTTTTTGGAAAATTTTCTGGGGGTTTTTC
15
+ CCCCTCTCCAAAAAGAAATGCAGGGTTTGTAAATTGTCATGAAAAAATCT
16
+ TTTCCTCTGAAATTTTTTTAAAAAAAAACAACTTCTGTAGCGACTTTTTG
17
+ CAGGCAGCGAAACCCCCCCCTGGCGACGGGTCCTTCTGCGGAAAAACCCA
18
+ TGTGTAAAAATACNCGGGAAAGCGCGGNACACCNNNTCGCATGTNNTGAT
19
+ TTGTATATTNNAGAAAAAAAGAAAGTGTCTCTCCTCGAGCTTATTAAAGA
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+ GGGGNTANGGGATGCCNAGAGGCCCCCNNTGTANNGNNTCTGTCGGGGGN
data/spec/testfiles/HA-mKSR1-KSRF5.txt ADDED
@@ -0,0 +1,20 @@
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+ >100122-36_O07_HA-mKSR1-KSRF5.ab1 950
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+ GGTTTTNTNACTGGCTGTGCTACCTGGCCCCGAGATCGTACGAGAAATGA
3
+ TCCCAGGGCGGGACGAGGACCAGCTGCCCTTCTCCAAAGCAGCCGATGTC
4
+ TATGCATTCGGGACTGTGTGGTATGAACTACAGGCAAGAGACTGGCCCTT
5
+ TAAGCACCAGCCTGCTGAGGCCTTGATCTGGCAGATTGGAAGTGGGGAAG
6
+ GAGTACGGCGCGTCCTGGCATCCGTCAGCCTGGGGAAGGAAGTCGGCGAG
7
+ ATCCTGTCTGCCTGCTGGGCTTTCGATCTGCAGGAGAGACCCAGCTTCAG
8
+ CCTGCTGATGGACATGCTGGAGAGGCTGCCCAAGCTGAACCGGCGGCTCT
9
+ CCCACCCTGGGCACTTTTGGAAGTCGGCTGACATTAACAGCAGCAAAGTC
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+ ATGCCCCGCTTTGAAAGGTTTGGCCTGGGGACCCTGGAGTCCGGTAATCC
11
+ AAAGATGTAGTGCGGCCGCCAGCACAGTGGCCATGGCATCTAGGGCGGCC
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+ AATTCCGCCCTCNTTCCCCCCCCACCCTCTCCCTCCCCCCTGTAACGTTA
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+ CTGGCCGAAGCCGCTTGGAATAAGGCCGGTGTGCGTTTGTCTATATGTTA
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+ TTTTCCACCATATTGCCGTCTTTTGGCAATGTGAGGGCCCGGAAACCTGG
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+ CCCTGTCTTCTTGACGAGCATTCCTAGGGGTCTTTCCCCTCTCGCCAAAG
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+ GAATGCAAGGTCTGTTGAATGTCGTGAAGGAAGCAGTTCCTCTGGAAGCT
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+ TCTTGAAGACAAACAACGTCTGTAGCGACCCTTTGCAGGCAGCGGAACCC
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+ CCCACCTGGCGACAGGTGCCTCTGCGGCCAAAAGCCACGTGTATAAGATA
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+ CACCTGCAAAGGCGGCACAACCCCAGTGCCACGTTGTGAGTTGGATAGTT
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+ GTGGAAAGAGTCAAATGGCTCTCCCTCAAGCGTATTCAACAAGGGGCTGA
data/spec/testfiles/HA-mKSR1-OXL33.txt ADDED
@@ -0,0 +1,20 @@
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+ >100122-36_E07_HA-mKSR1-OXL33.ab1 950
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+ CNCNCNNGNNCNNCCGCCCACGTGAAGGCTGCCGACCCCGGGGGTGGACCA
3
+ TCCTCTAGACTGCCGGATCCCAGTGTGGTGGTACGGGAATTATGTACCCA
4
+ TACGATGTTCCAGATTACGCTCTTATGGCCATGGAGGCCCGAATTCAAAT
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+ GGATAGAGCGGCGTTGCGCGCGGCAGCGATGGGCGAGAAAAAGGAGGGCG
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+ GCGGCGGGGGCGCCGCGGCGGATGGGGGCGCAGGGGCCGCCGTCAGCCGG
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+ GCGCTGCAGCAGTGCGGCCAGCTGCAGAAGCTCATCGATATCTCCATCGG
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+ CAGTCTGCGCGGGCTGCGCACCAAGTGCTCAGTGTCTAACGACCTCACAC
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+ AGCAGGAGATCCGGACCCTAGAGGCAAAGCTGGTGAAATACATTTGCAAG
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+ CAGCAGCAGAGCAAGCTTAGTGTGACCCCAAGCGACAGGACCGCCGAGCT
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+ CAACAGCTACCCACGCTTCAGTGACTGGCTGTACATCTTCAACGTGAGGC
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+ CTGAGGTGGTGCAGGAGATCCCCCAAGAGCTCACACTGGATGCTCTGCTG
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+ GAGATGGACGAGGCCAAAGCCAAGGAGATGCTGCGGCGCTGGGGGGCCAG
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+ CACGGAGGAGTGCAGCCGCCTACAGCAAGCCCTTACCTGCCTTCGGAAGG
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+ TGACTGGCCTGGGAGGGGAGCACAAAATGGACTCAGGTTGGAGTTCAACA
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+ GATGCTCGAGACAGTAGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCT
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+ GGGCAGAGCGGGTGCCAGCACTCAGGGACCCCGTTCCATCTCCGTGTCCG
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+ CCCTGCCTGCCTCAGACTCTCCGGTCCCCGGCCTCAGTGAGGGCCTCTCG
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+ GACTCCTGTATCCCCTTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCT
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+ GCACAGCTTCATCACGCCCCCTACCACACCCCAGCTACGACAGCACGCCA
data/spec/testfiles/KSR1_mouse_NM_013571_in_HA_pREX.ANNOTATED.fasta ADDED
@@ -0,0 +1,77 @@
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+ >HA-mKSR1-pREX-CD2 NM_013571.2
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+ # this is the leader found in the pRex vector
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+ GCTTGGATACACGCCGCCCACGTGAAGGCTGCCGACCCCGGGGGTGGACCATCCTCTAGACTGCC
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+ # BamHI
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+ GGATCC
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+ CAGTGTGGTGGTAGGGAATTA
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+ # this is the HA tag itself
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+ ATGTACCCATACGATGTTCCAGATTACGCT
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+ CTTATGGCCATGGAGGCCCGAATTC
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+ # not sure how to account for these two A's but there they are
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+ AA
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+ # EXTRA BAGGAGE:
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+ #GGTCGACCGAGATCTCTCGAGGTACC
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+ # NotI cleavage site
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+ #GCGGCCGC
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+ #CAGCACAGTGGCCATGGCATCTAG
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+ #This is the 5' UTR in mouse
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+ #CTCGGGGCTTTCCTGCCGAGGCGCCCGTGTCCCCGGGCTCCTCGCCTCGGCCCCCAGCGGCCCCGATGCCGAGGC
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+ #This is where translation actually begins:
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+ ATGGATAGAGCGGCGTTGCGCGCGGCAGCGATGGGCGAGAAAAAGGAGGGCGGCGGCGGGGGCGC
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+ CGCGGCGGACGGGGGCGCAGGGGCCGCCGTCAGCCGGGCGCTGCAGCAGTGCGGCCAGCTGCAGAAGCTC
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+ ATCGATATCTCCATCGGCAGTCTGCGCGGGCTGCGCACCAAGTGCTCAGTGTCTAACGACCTCACACAGC
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+ AGGAGATCCGGACCCTAGAGGCAAAGCTGGTGAAATACATTTGCAAGCAGCAGCAGAGCAAGCTTAGTGT
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+ GACCCCAAGCGACAGGACCGCCGAGCTCAACAGCTACCCACGCTTCAGTGACTGGCTGTACATCTTCAAC
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+ GTGAGGCCTGAGGTGGTGCAGGAGATCCCCCAAGAGCTCACACTGGATGCTCTGCTGGAGATGGACGAGG
26
+ CCAAAGCCAAGGAGATGCTGCGGCGCTGGGGGGCCAGCACGGAGGAGTGCAGCCGCCTACAGCAAGCCCT
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+ TACCTGCCTTCGGAAGGTGACTGGCCTGGGAGGGGAGCACAAAATGGACTCAGGTTGGAGTTCAACAGAT
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+ GCTCGAGACAGTAGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCTGGGCAGAGCGGGTGCCAGCACTC
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+ AGGGACCCCGTTCCATCTCCGTGTCCGCCCTGCCTGCCTCAGACTCTCCGGTCCCCGGCCTCAGTGAGGG
30
+ CCTCTCGGACTCCTGTATCCCCTTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCTGCACAGCTTCATC
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+ ACGCCCCCTACCACACCCCAGCTACGACGGCACGCCAAGCTGAAGCCACCAAGGACACCCCCACCGCCAA
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+ GCCGCAAGGTCTTCCAGCTGCTCCCCAGCTTCCCCACACTCACACGGAGCAAGTCCCACGAGTCCCAGCT
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+ GGGAAACCGAATCGACGACGTCACCCCGATGAAGTTTGAACTCCCTCATGGATCCCCACAGCTGGTACGA
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+ AGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAGGTGTGCAACGTGT
35
+ GCCAGAAGAGCATGATTTTTGGCGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAA
36
+ GGAAGCTCCCGCCTGCAGGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGGACAGAGTCTGTCCCGTCA
37
+ GATATCAACAACCCAGTGGACAGAGCAGCAGAGCCCCATTTTGGAACCCTTCCCAAGGCCCTGACAAAGA
38
+ AGGAGCACCCTCCAGCCATGAACCTGGACTCCAGCAGCAACCCATCCTCCACCACGTCCTCCACACCCTC
39
+ ATCGCCGGCACCTTTCCTGACCTCATCTAATCCCTCCAGTGCCACCACGCCTCCCAACCCGTCACCTGGC
40
+ CAGCGGGACAGCAGGTTCAGCTTCCCAGACATTTCAGCCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAG
41
+ CCGACAGTACACGGCTCGACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAGGCTGAGGA
42
+ GCCTGAGGCTGGCAAGTCAGAGGCAGAGGATGACGAGGAGGATGAGGTGGACGACCTCCCCAGCTCCCGC
43
+ CGGCCCTGGAGGGGCCCCATCTCTCGAAAGGCCAGCCAGACCAGCGTTTACCTGCAAGAGTGGGACATCC
44
+ CCTTTGAACAGGTGGAACTGGGCGAGCCCATTGGACAGGGTCGCTGGGGCCGGGTGCACCGAGGCCGTTG
45
+ GCATGGCGAGGTGGCCATTCGGCTGCTGGAGATGGACGGCCACAATCAGGACCACCTGAAGCTGTTCAAG
46
+ AAAGAGGTGATGAACTACCGGCAGACGCGGCATGAGAACGTGGTGCTCTTCATGGGGGCCTGCATGAACC
47
+ CACCTCACCTGGCCATTATCACCAGCTTCTGCAAGGGGCGGACATTGCATTCATTCGTGAGGGACCCCAA
48
+ GACGTCTCTGGACATCAATAAGACTAGGCAGATCGCCCAGGAGATCATCAAGGGCATGGGTTATCTTCAT
49
+ GCAAAAGGCATCGTGCACAAGGACCTCAAGTCCAAGAATGTCTTCTATGACAACGGCAAAGTGGTCATCA
50
+ CAGACTTCGGGCTGTTTGGGATCTCGGGTGTGGTCCGAGAGGAACGGCGCGAGAACCAACTGAAACTGTC
51
+ ACATGACTGGCTGTGCTACCTGGCCCCCGAGATCGTACGAGAAATGATCCCGGGGCGGGACGAGGACCAG
52
+ CTGCCCTTCTCCAAAGCAGCCGATGTCTATGCATTCGGGACTGTGTGGTATGAACTACAGGCAAGAGACT
53
+ GGCCCTTTAAGCACCAGCCTGCTGAGGCCTTGATCTGGCAGATTGGAAGTGGGGAAGGAGTACGGCGCGT
54
+ CCTGGCATCCGTCAGCCTGGGGAAGGAAGTCGGCGAGATCCTGTCTGCCTGCTGGGCTTTCGATCTGCAG
55
+ GAGAGACCCAGCTTCAGCCTGCTGATGGACATGCTGGAGAGGCTGCCCAAGCTGAACCGGCGGCTCTCCC
56
+ ACCCTGGGCACTTTTGGAAGTCGGCTGACATTAACAGCAGCAAAGTCATGCCCCGCTTTGAAAGGTTTGG
57
+ CCTGGGGACCCTGGAGTCCGGTAATCCAAAGATGTAGCCAGCCCTGCACGTTCATGCAGAGAGTGTCTTC
58
+ CTTTCGAAAACATGATCACGAAACATGCAGACCACCACCTCAAGGAATCAGAAGCATTGCATCCCAAGCT
59
+ GCGGACTGGGAGCGTGTCTCCTCCCTAAAGGACGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCG
60
+ TCACCAAGGTGTGTGGAGCTCAGGATCGCAGCCATACACGCAACTCCAGATGATACCACTACCGCCAGTG
61
+ TTTACACAGAGGTTTCTGCCTGGCAAGCTTGGTATTTTACAGTAGGTGAAGATCATTCTGCAGAAGGGTG
62
+ CTGGCACAGTGGAGCAGCACGGATGTCCCCAGCCCCCGTTCTGGAAGACCCTACAGCTGTGAGAGGCCCA
63
+ GGGTTGAGCCAGATGAAAGAAAAGCTGCGTGGGTGTGGGCTGTACCCGGAAAAGGGCAGGTGGCAGGAGG
64
+ TTTGCCTTGGCCTGTGCTTGGGCCGAGAACCACACTAAGGAGCAGCAGCCTGAGTTAGGAATCTATCTGG
65
+ ATTACGGGGATCAGAGTTCCTGGAGAGTGGACTCAGTTTCTGCTCTGATCCAGGCCTGTTGTGCTTTTTT
66
+ TTTTTCCCCCTTAAAAAAAAAAAAGTACAGACAGAATCTCAGCGGCTTCTAGACTGATCTGATGGATCTT
67
+ AGCCCGGCTTCTACTGCGGGGGGGAGGGGGGGAGGGATAGCCACATATCTGTGGAGACACCCACTTCTTT
68
+ ATCTGAGGCCTCCAGGTAGGCACAAAGGCTGTGGAACTCAGCCTCTATCATCAGACACCCCCCCCCAATG
69
+ CCTCATTGACCCCCTTCCCCCAGAGCCAAGGGCTAGCCCATCGGGTGTGTGTACAGTAAGTTCTTGGTGA
70
+ AGGAGAACAGGGACGTTGGCAGAAGCAGTTTGCAGTGGCCCTAGCATCTTAAAACCCATTGTCTGTCACA
71
+ CCAGAAGGTTCTAGACCTACCACCACTTCCCTTCCCCATCTCATGGAAACCTTTTAGCCCATTCTGACCC
72
+ CTGTGTGTGCTCTGAGCTCAGATCGGGTTATGAGACCGCCCAGGCACATCAGTCAGGGAGGCTCTGATGT
73
+ GAGCCGCAGACCTCTGTGTTCATTCCTATGAGCTGGAGGGGCTGGACTGGGTGGGGTCAGATGTGCTTGG
74
+ CAGGAACTGTCAGCTGCTGAGCAGGGTGGTCCCTGAGCGGAGGATAAGCAGCATCAGACTCCACAACCAG
75
+ AGGAAGAAAGAAATGGGGATGGAGCGGAGACCCACGGGCTGAGTCCCGCTGTGGAGTGGCCTTGCAGCTC
76
+ CCTCTCAGTTAAAACTCCCAGTAAAGCCACAGTTCTCCGAGCACCCAAGTCTGCTCCAGCCGTCTCTTAA
77
+ AACAGGCCACTCTCTGAGAAGGAATTC
data/spec/testfiles/testcase.fasta ADDED
@@ -0,0 +1,55 @@
1
+ >HA-mKSR1-pREX-CD2 NM_013571.2
2
+ # this is the leader found in the pRex vector
3
+ GCTTGGATACACGCCGCCCACGTGAAGGCTGCCGACCCCGGGGGTGGACCATCCTCTAGACTGCC
4
+ # BamHI
5
+ GGATCC
6
+ CAGTGTGGTGGTAGGGAATTA
7
+ # this is the HA tag itself
8
+ ATGTACCCATACGATGTTCCAGATTACGCT
9
+ CTTATGGCCATGGAGGCCCGAATTC
10
+ # not sure how to account for these two A's but there they are
11
+ AA
12
+ # EXTRA BAGGAGE:
13
+ #GGTCGACCGAGATCTCTCGAGGTACC
14
+ # NotI cleavage site
15
+ #GCGGCCGC
16
+ #CAGCACAGTGGCCATGGCATCTAG
17
+ #This is the 5' UTR in mouse
18
+ #CTCGGGGCTTTCCTGCCGAGGCGCCCGTGTCCCCGGGCTCCTCGCCTCGGCCCCCAGCGGCCCCGATGCCGAGGC
19
+ #This is where translation actually begins:
20
+ ATGGATAGAGCGGCGTTGCGCGCGGCAGCGATGGGCGAGAAAAAGGAGGGCGGCGGCGGGGGCGC
21
+ CGCGGCGGACGGGGGCGCAGGGGCCGCCGTCAGCCGGGCGCTGCAGCAGTGCGGCCAGCTGCAGAAGCTC
22
+ ATCGATATCTCCATCGGCAGTCTGCGCGGGCTGCGCACCAAGTGCTCAGTGTCTAACGACCTCACACAGC
23
+ AGGAGATCCGGACCCTAGAGGCAAAGCTGGTGAAATACATTTGCAAGCAGCAGCAGAGCAAGCTTAGTGT
24
+ GACCCCAAGCGACAGGACCGCCGAGCTCAACAGCTACCCACGCTTCAGTGACTGGCTGTACATCTTCAAC
25
+ GTGAGGCCTGAGGTGGTGCAGGAGATCCCCCAAGAGCTCACACTGGATGCTCTGCTGGAGATGGACGAGG
26
+ CCAAAGCCAAGGAGATGCTGCGGCGCTGGGGGGCCAGCACGGAGGAGTGCAGCCGCCTACAGCAAGCCCT
27
+ TACCTGCCTTCGGAAGGTGACTGGCCTGGGAGGGGAGCACAAAATGGACTCAGGTTGGAGTTCAACAGAT
28
+ GCTCGAGACAGTAGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCTGGGCAGAGCGGGTGCCAGCACTC
29
+ AGGGACCCCGTTCCATCTCCGTGTCCGCCCTGCCTGCCTCAGACTCTCCGGTCCCCGGCCTCAGTGAGGG
30
+ CCTCTCGGACTCCTGTATCCCCTTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCTGCACAGCTTCATC
31
+ ACGCCCCCTACCACACCCCAGCTACGACGGCACGCCAAGCTGAAGCCACCAAGGACACCCCCACCGCCAA
32
+ GCCGCAAGGTCTTCCAGCTGCTCCCCAGCTTCCCCACACTCACACGGAGCAAGTCCCACGAGTCCCAGCT
33
+ GGGAAACCGAATCGACGACGTCACCCCGATGAAGTTTGAACTCCCTCATGGATCCCCACAGCTGGTACGA
34
+ AGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAGGTGTGCAACGTGT
35
+ GCCAGAAGAGCATGATTTTTGGCGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAA
36
+ >100122-36_E07_HA-mKSR1-OXL33.ab1 950
37
+ CNCNCNNGNNCNNCCGCCCACGTGAAGGCTGCCGACCCCGGGGGTGGACCA
38
+ TCCTCTAGACTGCCGGATCCCAGTGTGGTGGTACGGGAATTATGTACCCA
39
+ TACGATGTTCCAGATTACGCTCTTATGGCCATGGAGGCCCGAATTCAAAT
40
+ GGATAGAGCGGCGTTGCGCGCGGCAGCGATGGGCGAGAAAAAGGAGGGCG
41
+ GCGGCGGGGGCGCCGCGGCGGATGGGGGCGCAGGGGCCGCCGTCAGCCGG
42
+ GCGCTGCAGCAGTGCGGCCAGCTGCAGAAGCTCATCGATATCTCCATCGG
43
+ CAGTCTGCGCGGGCTGCGCACCAAGTGCTCAGTGTCTAACGACCTCACAC
44
+ AGCAGGAGATCCGGACCCTAGAGGCAAAGCTGGTGAAATACATTTGCAAG
45
+ CAGCAGCAGAGCAAGCTTAGTGTGACCCCAAGCGACAGGACCGACCGAGCT
46
+ CAACAGCTACCCACGCTTCAGTGACTGGCTGTACATCTTCAACGTGAGGC
47
+ CTGAGGTGGTGCAGGAGATCCCCCAAGAGCTCACACTGGATGCTCTGCTG
48
+ GAGATGGACGAGGCCAAAGCCAAGGAGATGCTGCGGCGCTGGGGGGCCAG
49
+ CACGGAGGAGTGCAGCCGCCTACAGCAAGCCCTTACCTGCCTTCGGAAGG
50
+ TGACTGGCCTGGGAGGGGAGCACAAAATGGACTCAGGTTGGAGTTCAACA
51
+ GATGCTCGAGACAGTAGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCT
52
+ GGGCAGAGCGGGTGCCAGCACTCAGGGACCCCGTTCCATCTCCGTGTCCG
53
+ CCCTGCCTGCCTCAGACTCTCCGGTCCCCGGCCTCAGTGAGGGCCTCTCG
54
+ GACTCCTGTATCCCCTTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCT
55
+ GCACAGCTTCATCACGCCCCCTACCACACCCCAGCTACGACAGCACGCCA
metadata ADDED
@@ -0,0 +1,99 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: dna_sequence_aligner
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.0.2
5
+ platform: ruby
6
+ authors:
7
+ - John T. Prince
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+
12
+ date: 2010-02-12 00:00:00 -07:00
13
+ default_executable:
14
+ dependencies:
15
+ - !ruby/object:Gem::Dependency
16
+ name: bio
17
+ type: :runtime
18
+ version_requirement:
19
+ version_requirements: !ruby/object:Gem::Requirement
20
+ requirements:
21
+ - - ">="
22
+ - !ruby/object:Gem::Version
23
+ version: "0"
24
+ version:
25
+ - !ruby/object:Gem::Dependency
26
+ name: spec-more
27
+ type: :development
28
+ version_requirement:
29
+ version_requirements: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - ">="
32
+ - !ruby/object:Gem::Version
33
+ version: "0"
34
+ version:
35
+ description: does high pairwise alignment of sequencing reads with a template using bioruby and clustalw. gives template-centric output.
36
+ email: jtprince@gmail.com
37
+ executables:
38
+ - dna_sequence_aligner
39
+ - dna_translator.rb
40
+ extensions: []
41
+
42
+ extra_rdoc_files:
43
+ - LICENSE
44
+ - README.rdoc
45
+ files:
46
+ - .gitignore
47
+ - History
48
+ - LICENSE
49
+ - README.rdoc
50
+ - Rakefile
51
+ - VERSION
52
+ - bin/dna_sequence_aligner
53
+ - bin/dna_translator.rb
54
+ - lib/bio/alignment/dna_sequence.rb
55
+ - older/align_all.rb
56
+ - older/align_to_template.rb
57
+ - reference/clustalw_opts.txt
58
+ - script/fasta_compile_annotated.rb
59
+ - spec/align_spec.rb
60
+ - spec/spec_helper.rb
61
+ - spec/testfiles/HA-mKSR1-KSRF1.txt
62
+ - spec/testfiles/HA-mKSR1-KSRF2.txt
63
+ - spec/testfiles/HA-mKSR1-KSRF3.txt
64
+ - spec/testfiles/HA-mKSR1-KSRF4.txt
65
+ - spec/testfiles/HA-mKSR1-KSRF5.txt
66
+ - spec/testfiles/HA-mKSR1-OXL33.txt
67
+ - spec/testfiles/KSR1_mouse_NM_013571_in_HA_pREX.ANNOTATED.fasta
68
+ - spec/testfiles/testcase.fasta
69
+ has_rdoc: true
70
+ homepage: http://jtprince.github.com/dna_sequence_aligner
71
+ licenses: []
72
+
73
+ post_install_message:
74
+ rdoc_options:
75
+ - --charset=UTF-8
76
+ require_paths:
77
+ - lib
78
+ required_ruby_version: !ruby/object:Gem::Requirement
79
+ requirements:
80
+ - - ">="
81
+ - !ruby/object:Gem::Version
82
+ version: "0"
83
+ version:
84
+ required_rubygems_version: !ruby/object:Gem::Requirement
85
+ requirements:
86
+ - - ">="
87
+ - !ruby/object:Gem::Version
88
+ version: "0"
89
+ version:
90
+ requirements: []
91
+
92
+ rubyforge_project:
93
+ rubygems_version: 1.3.5
94
+ signing_key:
95
+ specification_version: 3
96
+ summary: does high pairwise alignment of sequencing reads with a template
97
+ test_files:
98
+ - spec/align_spec.rb
99
+ - spec/spec_helper.rb