AlignmentTools.jar pairwise-knn output

[sheikki]

I'm classifying representative sequences of quality controlled and clustered 16S reads with command:

java -jar AlignmentTools.jar pairwise-knn query.fq db.fa

The db file is unaligned prokaryotic subset of RDP 11.4 clustered at 99% (with some sequence length thresholds).

Is this a sensible way to assign taxonomy to my representative sequences?

In output, I see lines like:
@650A9:00200:00424 1 + 155 1.000 0 34 34 0 83 S004055894 Listeria monocytogenes; CA5 Lineage=Root;rootrank;Bacteria;domain;Firmicutes;phylum;Bacilli;class;Bacillales;order;Listeriaceae;family;Listeria;genus

As far as I can tell it's QID KNEIGHBOURS STRAND SCORE %ID QSTART QEND QEND QSTART SSTART SID. Is this the correct interpretation? Why is it that the QSTART and QEND values are displayed twice?

[rdpstaffmsu]

Hi, sheikki,

The columns definition is in the header of the output file:

#seqname k orientation score ident query_start query_end query_length
ref_start ref_end ref_seqid ref_desc

Is "@650A9:00200:00424" a sequence of length 34? If so, this assignment
might be your best bet, but it is too short to be reliable.

Benli Chai

RDP Staff

On Wed, May 11, 2016 at 5:48 AM, sheikki [email protected] wrote:

I'm classifying representative sequences of quality controlled and
clustered 16S reads with command:

java -jar AlignmentTools.jar pairwise-knn query.fq db.fa

The db file is unaligned prokaryotic subset of RDP 11.4 clustered at 99%
(with some sequence length thresholds).

Is this a sensible way to assign taxonomy to my representative sequences?

In output, I see lines like:

@650A9:00200:00424 1 + 155 1.000 0 34 34 0 83 S004055894 Listeria
monocytogenes; CA5
Lineage=Root;rootrank;Bacteria;domain;Firmicutes;phylum;Bacilli;class;Bacillales;order;Listeriaceae;family;Listeria;genus

As far as I can tell it's QID KNEIGHBOURS STRAND SCORE %ID QSTART QEND
QEND QSTART SSTART SID. Is this the correct interpretation? Why is it that
the QSTART and QEND values are displayed twice?

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RDP Staff
Ribosomal Database Project
Center for Microbial Ecology
Michigan State University
567 Wilson Rd. Room 2225 A
East Lansing, MI 48824
(517) 353-3842

[sheikki]

Thank you for the reply. Oddly, in my alignment file, ref_start value is always zero. A few examples:

@650A9:00007:00316  1   -   265 0.940   0   72  72  0   427 S001099040  Bacillus subtilis; XN-80-5  Lineage=Root;rootrank;Bacteria;domain;Firmicutes;phylum;Bacilli;class;Bacillales;order;Bacillaceae 1;family;Bacillus;genus
>-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAGCAACATCTTGCACGGTACTGACT-ACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>CACGTGGGTAACCTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGGCTAATACCGGATGGTTGTTTGAACCGCATGGTTCAGACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGGCGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGTAAGAACAAGTGCCGTTCAAATA-GGGCGGCACCTTG-ACGGTAC---CTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGACAATCCTAAGAGATAGGACGTCCCCTTCGGGGCAAGGTGACAGGTGGTGGCATTAGGAAGACAAGTCGTTCAATAAGCGGCACTTGACGGTACTACCAGAAAGGCCACGCTAACTACGTGCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTGTCGGAATATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTTCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGACAATCCTAGAGATAGGACGTCCCCTTCGGGGGCAGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGATCTTAGTTGCCAGCATTCAGTTGGGCACTCTAAGGTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGGCAGAACAAAGGGCAGCGAAACCGCGAGGTTAAGCCAATCCCACAAATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGGAATCGTTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCG
@650A9:00009:00308  1   -   449 1.000   0   102 102 0   515 S003301453  Bacillus cereus; B16    Lineage=Root;rootrank;Bacteria;domain;Firmicutes;phylum;Bacilli;class;Bacillales;order;Bacillaceae 1;family;Bacillus;genus
>---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTCTGGTTGTTAGGG-AGAACAAGTAGCTAG-T-AATAGCTGGCACCTTGACGGTACCTAA-CAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>TATTTGGGCGGGGGGGGGCCTATCATGCAGTCGAGCGAATGGATTAAGAGCTTGCTCTTATGAAGTTATCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCCATAAGACTGGGATAACTCCGGGAAACCGGGGCTCTAATACCGGATAACATTTTGAACCGCATGGTTCGAAATTGAAAGGCGGCTTCGGCTGTCACTTATGGATGGACCCGCGTCGCATTAACTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGGCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAACTCT-GTTGTTAGGGAAGAACAAGT-GCTAGTTGAATAGCTGGCACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGAGGGTTTCCGCCCTTTAGTGCTGAAGTTAACGCATTAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTAATTCGAAGCAACGCGAAGAACCCTACCAGGTCTTGACATCCTCTGAAACCCTAGAGATAGGGCTTCTCCTTCGGGAGCAGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGTTAAGTCCGCAACGAGCGCAACCCTTGATCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGGTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGACGGTACAAAGAGCTGCAAGACCGCGAGGTGGAGCTATTCTCATAAAACCGTTCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGCTGGAATCGCTAGTAATCGCGGATCAGGTTACCGCGGTGAATACGTTCCCGGGCCTTGTACACACCTCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTCGGTGGGGTAACCTTTTGGGAGCCAGCCGGCCTAAAGGGGGAGAAAG