[Bioperl-l] standaloneblastplus
sally roberts
elanorbust2 at yahoo.com
Fri Sep 10 15:13:08 UTC 2010
I think that is just a email error. Thanks for looking though!
--- On Thu, 9/9/10, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:
From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
Subject: RE: [Bioperl-l] standaloneblastplus
To: "'sally roberts'" <elanorbust2 at yahoo.com>, "'bioperl-l at lists.open-bio.org'" <bioperl-l at lists.open-bio.org>
Date: Thursday, September 9, 2010, 6:54 PM
Is that a typo in your email or are some of your fasta headers in your db incorrect?
Eg.
>301333052|GU725063|Xiphinema adenohystherum internal transcribed
>301333052|GU725063|spacer 1
AAAGACGAAAAATATATACTTTCTCACCGAAATATCAGACTATTCGGTTCCGATTTGATTCGCGGTAAGGCGCGCTAGCGCGGTAGCCCGCTATCGGTTCTGACTGTCTGGACCCCGAAAAATAGTAAGAAAGACGGTGTCGTCGGATCTCGGGTTAGTATTGTATATATCGGGGACTTATCGGTCTGT
Shouldn't that be:
>301333052|GU725063|Xiphinema adenohystherum internal transcribed spacer 1
AAAGACGAAAAATATATACTTTCTCACCGAAATATCAGACTATTCGGTTCCGATTTGATTCGCGGTAAGGCGCGCTAGCGCGGTAGCCCGCTATCGGTTCTGACTGTCTGGACCCCGAAAAATAGTAAGAAAGACGGTGTCGTCGGATCTCGGGTTAGTATTGTATATATCGGGGACTTATCGGTCTGT
Maybe the invalid fasta headers are breaking the db formatter?
Russell Smithies
Technical Support
T +64 3 489 9085
E russell.smithies at agresearch.co.nz
Invermay Research Centre
Puddle Alley,
Mosgiel,
New Zealand
T +64 3 489 3809
F +64 3 489 9174
www.agresearch.co.nz
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of sally roberts
> Sent: Friday, 10 September 2010 4:10 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] standaloneblastplus
>
> I am running a test for standaloneblastplus but getting data back that
> does not exist in my query or my local database. Below is a outline of my
> script small database, query list, and erroneous results. As you will
> notice the query list is comprised of the first four sequences found in
> the database. The results say it can not find the first two and then the
> mathces for the last two do not exist!
>
> Thanks for any help!
>
>
>
> Program
>
>
> #!/usr/bin/perl
>
> use Bio::Tools::Run::StandAloneBlastPlus;
>
>
> $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
> -db_name => 'ITS',
> -db_data => 'smallDB.fas',
> -create => 1
> );
>
> $result = $fac->blastn( -query => , 'sequences.fasta',
> -outfile => 'ITStest2.bls');
>
>
> smallDB.fas Data
>
> >302585252|HM807352|Waitea circinata internal transcribed spacer 1
> ATGATTGGTGGCTGTTGCTGGCTAGTGTTTCTAGTATGTGCACGCCACACCTTCAATCCCACTTACACCTGTGC
> ACCTTTTGTAGTATTACTTGTGGATATCGAGAGAAAGTTTAGTCTTTCACTCTGTTGAAACCGGTTTACTACGT
> TTTTTTATACACACACAATAGTCATTGAATGTATTTTTTATTTCTTATGATAAAAA
>
> >302585252|HM807352|Waitea circinata internal transcribed spacer 2
> GAATCTCTCAAATACAATAATTTTTTTTGATTGTTGTATTTGGACTTGGAAGCTGTTGGCGCAAGTCGACTCTT
> CTCAAATGTATTAGCTGGGGTTTATATAGTTGGATCCTTGGTGTGATAATTATCTACGCCTTGAAGTCCCTGTA
> GACTCTGCTTCAAATCGTCTCTTCATGAGACAATATTTGAATCA
>
> >302585250|HM802273|Fusarium oxysporum contains 18S ribosomal RNA,
> internal transcribed spacer 1, 5.8S ribosomal RNA, internal transcribed
> spacer 2, and 28S ribosomal RNA"
> CTCGAGGTCTTACCGAGTTTCACTCCCAACCCCTGTGAACATCACCAATTGTTGCCTCGGCGGATCAGCCCGCT
> CCCGGTAAAACGGGACGGCCCGCCAGAGGACCCCTAAACTCTGTTTCTATATGTAACTTCTGAGTAAAACCATA
> AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCAAAATGCGATAAGTA
> ATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCAT
> GCCTGTTCGAGCGTCATTTCAACCCTCAAGCCCCCGGGTTTGGTGTTGGGGATCGGCGAGCCCTTGCGGCAAGC
> CGGCCCCGAAATCTAGTGGCGGTCTCGCTGCAGCTTCCCCTGCATAGAAAACCCGCGGGGGGGGGAC
>
> >302585249|HM802272|Fusarium oxysporum contains 18S ribosomal RNA,
> internal transcribed spacer 1, 5.8S ribosomal RNA, internal transcribed
> spacer 2, and 28S ribosomal RNA"
> GAGGTCTTACCGAGTTTCACTCCCAACCCCTGTGAACATACCACTTGTTGCCTCGGCGGATCAGCCCGCTCCCG
> GTAAAACGGGACGGCCCGCCAGAGGACCCCTAAACTCTGTTTCTATATGTAACTTCTGAGTAAAACCATAAATA
> AATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCCAAATGCGATAAGTAATGT
> GAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCT
> GTTCGAGCGTCATTTCAACCCTCAAGCACAGCTTGGTGTTGGGACTCGCGTTAATTCGCGTTCCTCAAATTGAT
> TGTCGTTCACGTCGAGCTTCCATAGCGTAGTAGTAAAACCCTCGTTACTGGTAATCGTCGCGGCCACGCCGTTA
> AACCCCAACTTCTGAATGTTGACCTCGGATCAGTAAGGAATACCCGCTGAACTTAAGCATATCATTAAGCGGAG
> GAA
>
> >302585248|HM802271|Fusarium oxysporum contains 18S ribosomal RNA,
> internal transcribed spacer 1, 5.8S ribosomal RNA, internal transcribed
> spacer 2, and 28S ribosomal RNA"
> CCGAGGTCTTACCGAGTTTCACTCCCAACCCCTGTGAACATACCAATTGTTGCCTCGGCGGATCAGCCCGCTCC
> CGGTAAAACGGGACGGCCCGCCAGAGGACCCCTAAACTCTGTTTCTATATGTAACTTCTGAGTAAAACCATAAA
> TAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCAAAATGCGATAAGTAAT
> GTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGC
> CTGTTCGAGCGTCATTTCAACCCTCAAGCCCCCGGGTTTGGTGTTGGGGATCGGCGAGCCCTTGCGGCAAGCCG
> GCCCCGAAATCTAGTGGCGGTCTCGCTGCAGCTTCCATTGCGTAGTAGTAAAACCCTCGCAACTGGTACGCGGC
> GCGGCCAAGCCGTTAAACCCCCAACTTCTGAATGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGC
> ATATCATTAAAGCGGAGGAA
>
> >301333053|GU725064|Xiphinema turcicum internal transcribed spacer 1
> GGAGAGATTATATCTTTCTCGAAAAGAGAAAAAATATCCGAGCCGAGCGAACCGACCGAAAAACGCGGTGAGGC
> GCCTTTTGCGCAAAGTCCGTACGTCGGTTCTTAGCGAATATAGCCTCGGCCTGGGACCCGAAAGATGTTTCCTA
> TATGTATCTCGAGACCGACCGTTTAAGACGGTAGCCGGAAAAAAGATTATACCGTGGGTGAAGGTGTCGAAAAG
> AATAATGTAGGTAAAAAAGAAAGACAGACAGAGGAGAGAAAGAACGAAAGTAGAACTCGAACGTAGTTTGAGCT
> ACGCAGTAACGGTATCCGTCGTGGGACATCGCGGTGCGTCGGTTGTAGGGAGTTAAGATTACCTACCCGACACC
> TCGATATTAATCCCGCGCGAATAAATGCGGATTACCGTGAATGTACGCTCTGCTTCGATATCGGGCTTCTTTTG
> ACACCGAAAATATATATATGAATAAAAATAAAGTCACCCTCGTTGCAACGGTATATATCAAAGCGGTTTTCCGT
> GAAAAGAAAGAAGGCGGCTTCGGTTCTCGTTATATTAGGAATAATCTAAGTAATTTCAGACGTCCCGGGAATCG
> TTACTATAGATAGAGAGCGATAGTAACGGTTTCTCCTTCGGGTACTTATCGAACGTTAACACTGCGGTAATCCG
> TCTGGCCGCAAGGAGAGAGGTGTTACGTTCGGCAGCCCTAAATTTCGACCCGTTCGACTAATGCGACGGCCCTA
> CCGAGAAAATGTAGGGCCTATGTACATAGTCCGAAAGAAATACGATCGGAATATTAAGGGTTAGGTTTAAAGAG
> TCATCGGTTCCGAGTACGCGTTCGTTCGGCACGATGCGTGTGTGTATATATCGTAGAGGAGTATTGACGATATA
> TATGTATGCGTATTCGCCCTTACGATAAGAGAATATCGCGTAATTCGGAGCGGCCGTTCTTCGCGAGAGAGAGA
> ACGCA
> CGCGTTAGAAGCTTACGAGTCGGTGTTAAGTTCGAAGGAGAGAGGTTCGAACCGAAGCCGGCGAGTACGCGTTA
> AGTCGTTTCGCGAGAGACGGTCCGGGACGAAAAGGAGAGAGTATCGTCCGGGTGTCCGCCCGAAATAGATATCT
> TATCGAGAATATTTTTATATAGTTCGTTAGAAAGAATGCGAACTTTAAA
>
> >301333052|GU725063|Xiphinema adenohystherum internal transcribed spacer
> 1
> AAAGACGAAAAATATATACTTTCTCACCGAAATATCAGACTATTCGGTTCCGATTTGATTCGCGGTAAGGCGCG
> CTAGCGCGGTAGCCCGCTATCGGTTCTGACTGTCTGGACCCCGAAAAATAGTAAGAAAGACGGTGTCGTCGGAT
> CTCGGGTTAGTATTGTATATATCGGGGACTTATCGGTCTGTCGAGTTTCTTTCCGGGGTTCTTTGAGTTTATTG
> GGACAGTGTCGGTTGTAGCGGAGTTTGGATACCTACCCGACTGTCCTTATAGTCTCGTGAACACGAGCCCGGGA
> ATAGAAGAGACTCGGCTGATAACGACCGACTATATCTCGTTATATACTCAGAGTTGAATAACTGAGTGGCTCGA
> AACGGCGACATTGTACTTACTATTTTATGTAGACTCTGGAAATATCAGACGTCCCGGGGAATCGTTACAGAGGA
> AATATAGGGTACCTGGAAAAAGAATGGTACCCGTTCCTGTAATGATTCCTTATTCGGGTACCTATCGAATACTA
> ACGGCGCGGATCCCCCGTCTGGCCGCGACGGAATAAGCGTTAGATTCGGTATCCCTATATTCGCGAGTATTCGA
> CTAGTCATGAAATAGAGCCCTTATCGGGGTATCGACTGTCGATCGGATAGAAAGCGAATTAGGGTTAGGTTTAA
> AGAGTCATTGGTTCCGTATATATGGGTGGAACGTACCCGTAAAGGAACAGCCGTAGACGCGAGTTCGGAAATAA
> GTATATTCTCGCGAGAAAGAGGGTCCGTGTACCTTCAAGGTACTTGAATTTAGACCCAGTCTCGTGAATATACG
> TAACTCGTCGAATGGCTCGGGACATGTAGAATACTATGTCCGGGTGACCGCCCGAAATAAGAATATTCATCAGA
> AACTTTTATATATAGTTCGCCGAATAATAGCGAAC
>
> >301333051|GU725062|Xiphinema sphaerocephalum internal transcribed spacer
> 1
> AAAGTCGAAAAAATATACTTTCTCGCGGAGAAATAATACGGACCGTTCAGTCCGACTCTATACGCGGTAAGGCG
> CTCTTGCGCGAGAGCCCGCTGTCGGTTCTGACGGTCCGGACCCCGAAAAGTAGTAAGTACGACTACGATATATC
> GTGGTCGAGTATCGGTTAGTAATAGTATATCGGGACTGACCGATCGGTCGGTCGAGTTTCTACCGGCTTCTTTG
> AGTCTATTCGGGCAGCGTCGGTTGTAGCGGAGTTTGGATACCTACCCGACTGTCCTTGTAGAACTCGTGAATTC
> GAGCTCGGTAACCGGGAACTCGGCTGAGAACGACCGATTACTTCTCGATACGCTCGAACGTATATATCTAACCG
> AGAAAAGGCGACGTTGTACTTACTATTTATATCAGACGTCCCGAGAGTCGTTACGGTCGGAAATATTGGGTACC
> GGTATCGGACCCGTTTCCGTATCGGCTCTTTATTCGGGTACCTATCGAATACTAACGCCGCGGTTCACCGTCTG
> GCCGCGACGGAATACGCGTTAGATTCGGCACCCCCTATATTCGTATATATATCGACTAGTCTCGAAATAGAGCC
> CTTACTAGGGTGAAGACTATGTCGATCGGAAAGAATCGGATTAGGGGTAGGTTTAAAGAGTCATCGGTTCCGTG
> TATCCGGGCGAAATATATACCCGTAACGGAACGACCGTTGACGCGAGTTTGAAGATATATACATGTACGTATAT
> GAGACAAAAAAACGAGGGTCTGTACCGTGAATTTTTTAGGTACCGAAAAGAGGACCCCCGGTCTCGTGAATATG
> TATTACTCGCCGAACGGTTCGGGACATGGAGAATATTATGTCCGGGTGACCGCCCGAAATAGAAATTTTTTTCT
> ATAAAGTTTTGATATACGTATAGTTCGTCGAATAAAAGC
>
> >301333050|GU725061|Xiphinema hispanum internal transcribed spacer 1
> AAAGCCGAAAAATATATACTTTCTCAGAGAAATACTAGACTAGTCGATTCCGACTTGATTCGCGGTAAGGCGCT
> TTCGCGCGATAGCCCGCTGTCGGTTCCGACCGTCTGGACCCCGAAAAATAGTAAGAACGACGGTGTCGTCGATC
> TCGGTTAGAAATTGTATATATGTCGGGACGGATCGGTCGGTCGAGTTCCTTTCGGTGTTCTTAGAGTTTATTCG
> GGCAGTGTCGGTTGTAGCGGAGTTTGGATACCTACCCGACTGTCCTTATAATCTCGTGAACTTAGAACCCGGAA
> TAGAGGGAACTCGGCTGATAACGACCGACTTATGTCTCGCCGTATACCGTGAGTTATTTGACCGAGTGGCTCGA
> AACGGCGGTATTGTACTTACTATTTATCTAGTCTCTGGAAATATCAGACGTCCCGGGAATCGTTACAGCGGAAA
> TATAGGGTACCCGAAAAACTGGTACCCGTTTCTGAAACGACTCCTTATTCGGGTACCTATCGAATACTAACGCC
> GCAGTTTCCCGTCTGGCTGCGATGGAAAAAGCGTTAGATTCGGGATCTCTATATTCGCGGGTGTTCGATTAGTC
> GTGAAATACAGCCCTTACGCGGGTGACGACGGTCGATCGGAAAGAAAGCGAATTAGGGTTAGGTTTAAAGAGTC
> ATTGGTTCCGTGTACGGGCGAAAAAGTACCCGTTACGGAACGGCCGTCGACGCGAGTGTGGAAATAAGTATATA
> GTTACGAGAAAGAGGGTCTGTACCTCGGAGTTTTTTGAAGGTACCGTAATCAGGACCCTGTCTCGTGAATATAC
> AAGTTACTCGCCGAACGGTTCGGCCAATGTAGAATTTTATGTCCGGGTGACCGCCCGAAATAGAAATATTTCAT
> AAAAAGCTTTTATATATAGTTTGCCGAATAATAGCAAACG
>
> >301333049|GU725060|Xiphinema pyrenaicum internal transcribed spacer 1
> AAAGCGGAAAAATTACTTTCTCACCCGGAAAAAACAGACCGTTTATCGGTCCGACTTGAAACGCGGTAAGGCGC
> TCTTGCGCGATAGCCCGCCGTCGGTTCCGATGGTCTGGACCCCGAAAAATAGTAAGAACGACGGTGTCGTCGAT
> TCTCGGTTAGTAGTATATCCGGTCGGATCGATATATATCGGTCGGTCGAGTTTCTATCGGGTTCTTTGAGTTTC
> TTCGGACAGCGTCGGTTGTAGTGGAGTTTGGATACCTACCCGACTGTCCTTATAATCTCGTGAACTCTAGCCCG
> ATAATAATACGGAACTCGGCTGAGAACGACCGACTTAGGTCTGAGTAGATATACTGAGAATATTACCTAGCCGA
> GATGAACGAAACGGCGACATTGGAGTTTTACTATTTACTCGTATCAGACGTCCCGGGAATCGTTGCAGTTGAAT
> TACATATATACGGGTACCTGTAATTGGACTCGTTTCTGTAACGGTTCTTTAGTCGGGTACCTATCGAATACTAA
> CGCCGCGGTTATCCGTCTGGCCGCGATGGAATAAGCGTTAGATTCGGCATCCCTTTATTCGTATACGTTCGAGT
> AGTCGTGAATTAGAACCCTTTAACCGGGGTGAAGACTATCGACGGGAGATAAGCGAATTAGGGGTAGGTTTAAA
> GAGTCATCGGTTCCGGATACGGAGAGAAAAATGCCCGTAATGGAACGACCATTGAAGCGGGATCTATATATATA
> TATATATGATTCGCCCGATGGTTCGGGACATGGAGAATTTTATGTCCGGGTGACCGCCCGAAATAGAAATATTT
> ACTTCAAAGTTATTTATATATAGTTCGCCTTATAAGAGCGAACG
>
>
>
> sequences.fasta data
>
> >Test1
> ATGATTGGTGGCTGTTGCTGGCTAGTGTTTCTAGTATGTGCACGCCACACCTTCAATCCCACTTACACCTGTGC
> ACCTTTTGTAGTATTACTTGTGGATATCGAGAGAAAGTTTAGTCTTTCACTCTGTTGAAACCGGTTTACTACGT
> TTTTTTATACACACACAATAGTCATTGAATGTATTTTTTATTTCTTATGATAAAAA
>
> >Test2
> GAATCTCTCAAATACAATAATTTTTTTTGATTGTTGTATTTGGACTTGGAAGCTGTTGGCGCAAGTCGACTCTT
> CTCAAATGTATTAGCTGGGGTTTATATAGTTGGATCCTTGGTGTGATAATTATCTACGCCTTGAAGTCCCTGTA
> GACTCTGCTTCAAATCGTCTCTTCATGAGACAATATTTGAATCA
>
> >Test3
> CTCGAGGTCTTACCGAGTTTCACTCCCAACCCCTGTGAACATCACCAATTGTTGCCTCGGCGGATCAGCCCGCT
> CCCGGTAAAACGGGACGGCCCGCCAGAGGACCCCTAAACTCTGTTTCTATATGTAACTTCTGAGTAAAACCATA
> AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCAAAATGCGATAAGTA
> ATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCAT
> GCCTGTTCGAGCGTCATTTCAACCCTCAAGCCCCCGGGTTTGGTGTTGGGGATCGGCGAGCCCTTGCGGCAAGC
> CGGCCCCGAAATCTAGTGGCGGTCTCGCTGCAGCTTCCCCTGCATAGAAAACCCGCGGGGGGGGGAC
>
> >Test4
> GAGGTCTTACCGAGTTTCACTCCCAACCCCTGTGAACATACCACTTGTTGCCTCGGCGGATCAGCCCGCTCCCG
> GTAAAACGGGACGGCCCGCCAGAGGACCCCTAAACTCTGTTTCTATATGTAACTTCTGAGTAAAACCATAAATA
> AATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCCAAATGCGATAAGTAATGT
> GAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCT
> GTTCGAGCGTCATTTCAACCCTCAAGCACAGCTTGGTGTTGGGACTCGCGTTAATTCGCGTTCCTCAAATTGAT
> TGTCGTTCACGTCGAGCTTCCATAGCGTAGTAGTAAAACCCTCGTTACTGGTAATCGTCGCGGCCACGCCGTTA
> AACCCCAACTTCTGAATGTTGACCTCGGATCAGTAAGGAATACCCGCTGAACTTAAGCATATCATTAAGCGGAG
> GAA
>
>
>
>
> Results
>
> BLASTN 2.2.24+
>
>
> Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
> Miller (2000), "A greedy algorithm for aligning DNA sequences", J
> Comput Biol 2000; 7(1-2):203-14.
>
>
>
> Database: ITS
> 5 sequences; 1,102 total letters
>
>
>
> Query= Test1
> Length=204
>
>
> ***** No hits found *****
>
>
>
> Lambda K H
> 1.33 0.621 1.12
>
> Gapped
> Lambda K H
> 1.28 0.460 0.850
>
> Effective search space used: 202071
>
>
> Query= Test2
> Length=192
>
>
> ***** No hits found *****
>
>
>
> Lambda K H
> 1.33 0.621 1.12
>
> Gapped
> Lambda K H
> 1.28 0.460 0.850
>
> Effective search space used: 189507
>
>
> Query= Test3
> Length=437
>
> Score E
> Sequences producing significant alignments:
> (Bits) Value
>
> dbj|AB581518.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5...
> 300 2e-085
> dbj|AB581521.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5...
> 69.4 6e-016
> dbj|AB581519.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5...
> 58.4 1e-012
> dbj|AB581522.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5...
> 56.5 4e-012
>
>
> >dbj|AB581518.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5.8S rRNA,
> partial
> sequence, clone: G59F
> Length=203
>
> Score = 300 bits (162), Expect = 2e-085
> Identities = 176/182 (96%), Gaps = 4/182 (2%)
> Strand=Plus/Plus
>
> Query 10 TTACCGAGTTT-C-ACTCCC-AACCCCTGTGAACATCACCAATTGTTGCCTCGGCGGATC
> 66
> ||||||||||| | |||||| |||||| |||||||| |||| ||||||||||||||||||
> Sbjct 23 TTACCGAGTTTACAACTCCCAAACCCCAGTGAACAT-ACCACTTGTTGCCTCGGCGGATC
> 81
>
> Query 67 AGCCCGCTCCCGGTAAAACGGGACGGCCCGCCAGAGGACCCCTAAACTCTGTTTCTATAT
> 126
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct 82 AGCCCGCTCCCGGTAAAACGGGACGGCCCGCCAGAGGACCCCTAAACTCTGTTTCTATAT
> 141
>
> Query 127 GTAACTTCTGAGTAAAACCATAAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCT
> 186
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct 142 GTAACTTCTGAGTAAAACCATAAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCT
> 201
>
> Query 187 GG 188
> ||
> Sbjct 202 GG 203
>
>
> >dbj|AB581521.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5.8S rRNA,
> partial
> sequence, clone: G64F
> Length=217
>
> Score = 69.4 bits (37), Expect = 6e-016
> Identities = 39/40 (97%), Gaps = 0/40 (0%)
> Strand=Plus/Plus
>
> Query 149 AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG 188
> ||||| ||||||||||||||||||||||||||||||||||
> Sbjct 178 AATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGG 217
>
>
> >dbj|AB581519.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5.8S rRNA,
> partial
> sequence, clone: G60F
> Length=206
>
> Score = 58.4 bits (31), Expect = 1e-012
> Identities = 39/42 (92%), Gaps = 3/42 (7%)
> Strand=Plus/Plus
>
> Query 146 ATAA-ATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCT 186
> |||| || ||| ||||||||||||||||||||||||||||||
> Sbjct 165 ATAACAT-AAT-AAAACTTTCAACAACGGATCTCTTGGTTCT 204
>
>
> >dbj|AB581522.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5.8S rRNA,
> partial
> sequence, clone: G65F
> Length=256
>
> Score = 56.5 bits (30), Expect = 4e-012
> Identities = 30/30 (100%), Gaps = 0/30 (0%)
> Strand=Plus/Plus
>
> Query 157 AAAACTTTCAACAACGGATCTCTTGGTTCT 186
> ||||||||||||||||||||||||||||||
> Sbjct 225 AAAACTTTCAACAACGGATCTCTTGGTTCT 254
>
>
>
> Lambda K H
> 1.33 0.621 1.12
>
> Gapped
> Lambda K H
> 1.28 0.460 0.850
>
> Effective search space used: 442850
>
>
> Query= Test4
> Length=521
>
> Score E
> Sequences producing significant alignments:
> (Bits) Value
>
> dbj|AB581518.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5...
> 309 4e-088
> dbj|AB581521.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5...
> 69.4 7e-016
> dbj|AB581519.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5...
> 58.4 1e-012
> dbj|AB581522.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5...
> 56.5 5e-012
>
>
> >dbj|AB581518.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5.8S rRNA,
> partial
> sequence, clone: G59F
> Length=203
>
> Score = 309 bits (167), Expect = 4e-088
> Identities = 177/181 (97%), Gaps = 3/181 (1%)
> Strand=Plus/Plus
>
> Query 7 TTACCGAGTTT-C-ACTCCC-AACCCCTGTGAACATACCACTTGTTGCCTCGGCGGATCA
> 63
> ||||||||||| | |||||| |||||| ||||||||||||||||||||||||||||||||
> Sbjct 23 TTACCGAGTTTACAACTCCCAAACCCCAGTGAACATACCACTTGTTGCCTCGGCGGATCA
> 82
>
> Query 64 GCCCGCTCCCGGTAAAACGGGACGGCCCGCCAGAGGACCCCTAAACTCTGTTTCTATATG
> 123
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct 83 GCCCGCTCCCGGTAAAACGGGACGGCCCGCCAGAGGACCCCTAAACTCTGTTTCTATATG
> 142
>
> Query 124 TAACTTCTGAGTAAAACCATAAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTG
> 183
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct 143 TAACTTCTGAGTAAAACCATAAATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTG
> 202
>
> Query 184 G 184
> |
> Sbjct 203 G 203
>
>
> >dbj|AB581521.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5.8S rRNA,
> partial
> sequence, clone: G64F
> Length=217
>
> Score = 69.4 bits (37), Expect = 7e-016
> Identities = 39/40 (97%), Gaps = 0/40 (0%)
> Strand=Plus/Plus
>
> Query 145 AATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG 184
> ||||| ||||||||||||||||||||||||||||||||||
> Sbjct 178 AATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGG 217
>
>
> >dbj|AB581519.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5.8S rRNA,
> partial
> sequence, clone: G60F
> Length=206
>
> Score = 58.4 bits (31), Expect = 1e-012
> Identities = 39/42 (92%), Gaps = 3/42 (7%)
> Strand=Plus/Plus
>
> Query 142 ATAA-ATAAATCAAAACTTTCAACAACGGATCTCTTGGTTCT 182
> |||| || ||| ||||||||||||||||||||||||||||||
> Sbjct 165 ATAACAT-AAT-AAAACTTTCAACAACGGATCTCTTGGTTCT 204
>
>
> >dbj|AB581522.1| Uncultured fungus genes for 18S rRNA, ITS1 and 5.8S rRNA,
> partial
> sequence, clone: G65F
> Length=256
>
> Score = 56.5 bits (30), Expect = 5e-012
> Identities = 30/30 (100%), Gaps = 0/30 (0%)
> Strand=Plus/Plus
>
> Query 153 AAAACTTTCAACAACGGATCTCTTGGTTCT 182
> ||||||||||||||||||||||||||||||
> Sbjct 225 AAAACTTTCAACAACGGATCTCTTGGTTCT 254
>
>
>
> Lambda K H
> 1.33 0.621 1.12
>
> Gapped
> Lambda K H
> 1.28 0.460 0.850
>
> Effective search space used: 530378
>
>
> Database: ITS
> Posted date: Aug 27, 2010 9:43 AM
> Number of letters in database: 1,102
> Number of sequences in database: 5
>
>
>
> Matrix: blastn matrix 1 -2
> Gap Penalties: Existence: 0, Extension: 2.5
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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