[Bioperl-l] standaloneblastplus
Dave Messina
David.Messina at sbc.su.se
Fri Sep 10 16:23:26 UTC 2010
Hi Sally,
Did you run the same search on the command line, outside of BioPerl?
The issue you're having may be with Blast+ and not BioPerl. For example, it's possible that the low-complexity and compositional matrix adjustment filtering (which are turned on by default) are excluding the expected matches.
Dave
On Sep 10, 2010, at 17:13 , sally roberts wrote:
> 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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