Re: [GUSDEV] [ApiDB] dots.source table and genbank source qualifiers

[Chris S. <sto...@pc...>]

Hi Haiming,
Another view of NAFeature used to handle GenBank qualifiers (that we  
were not using at the time the DoTS schema was created) is  
DoTS.Miscellaneous
http://www.gusdb.org/SchemaBrowser/table.htm? 
schema=DoTS&table=Miscellaneous
Note that most of the columns are of type string so some of this  
information could be packed into EVIDENCE or PCR_CONDITIONS.  Between  
that view and DoTS.Source you might find a field to put things. Not a  
clean solution but may be sufficient for now.

What is the anticipated use of those pieces of information? Is this  
primarily archival? descriptive? Or will there be queries of the  
nature: provide all isolates from the USA collected after the year  
2000? For the first two cases, proper structuring is less urgent but  
for the latter we would certainly want to add the appropriate  
attributes. Frank is working on a 3.6 version of GUS and this could  
be a candidate for inclusion.

Cheers,
Chris

Chris Stoeckert, Ph.D.
Research Professor, Dept. of Genetics
1415 Blockley Hall, Center for Bioinformatics
423 Guardian Dr., University of Pennsylvania
Philadelphia, PA 19104
Ph: 215-573-4409 FAX: 215-573-3111
http://www.cbil.upenn.edu


On Oct 4, 2007, at 11:08 AM, Haiming Wang wrote:

> Hi,
>
> I'm loading isolate genbank records into GUS using  
> GUS::Supported::Plugin::InsertSequenceFeatures. It works well  
> except some qualifiers (under source) do not have corresponding  
> columns in DOTS.SOURCE table. Those qualifiers include "country,  
> collection_date, collected_by, environmental_sample, PCR_primers,  
> virion...", such as
>
> /organism="Cryptosporidium environmental sequence"
> /mol_type="genomic DNA"
> /isolation_source="environmental water sample"
> /db_xref="taxon:310753"
> /clone="JF#1"
> /environmental_sample
> /country="USA: Massachusetts"
> /collection_date="Jun-2001"
> /collected_by="Kristen Jellison"
> PCR_primers=fwd_name: CPB-DIAGF, rev_name:CPB-DIAGR"
> ...
>
> Please refer to the attached genbank file - 117671303.gb, for details
>
> I'd like to know if we intend to add those qualifier-match columns  
> in DOTS.SOURCE table.  Otherwise, we need several special handlers  
> to deal with them. Thanks for your inputs!
>
> -Haiming
>
>
> p.s. all the qualifiers in Genbank source
>
> Feature Key           source
>
> Mandatory qualifiers  /organism="text"
>                      /mol_type="genomic DNA", "genomic RNA", "mRNA"...
>                               Optional qualifiers   /cell_line="text"
>                      /cell_type="text"
>                      /chromosome="text"
>                      /citation=[number]
>                      /clone="text"
>                      /clone_lib="text"
>                      /collected_by="text"
>                      /collection_date="text"
>                      /country="<country_value>[:<region>][,  
> <locality>]"
>                      /cultivar="text"
>                      /db_xref="<database>:<identifier>"
>                      /dev_stage="text"
>                      /ecotype="text"
>                      /environmental_sample
>                      /focus
>                      /frequency="text"
>                      /germline
>                      /haplotype="text"
>                      /identified_by="text"
>                      /isolate="text"
>                      /isolation_source="text"
>                      /label=feature_label
>                      /lab_host="text"
>                      /lat_lon="text"
>                      /macronuclear
>                      /map="text"
>                      /note="text"
>                      /organelle=<organelle_value>
>                      /PCR_primers="[fwd_name: XXX, ]fwd_seq: xxxxx,
>                      [rev_name: YYY, ]rev_seq: yyyyy"
>                      /plasmid="text"
>                      /pop_variant="text"
>                      /proviral
>                      /rearranged
>                      /segment="text"
>                      /serotype="text"
>                      /serovar="text"
>                      /sex="text"
>                      /specimen_voucher="text"
>                      /specific_host="text"
>                      /strain="text"
>                      /sub_clone="text"
>                      /sub_species="text"
>                      /sub_strain="text"
>                      /tissue_lib="text"
>                      /tissue_type="text"
>                      /transgenic
>                      /variety="text"
>                      /virion
> LOCUS       EF060289                 425 bp    DNA     linear   ENV  
> 14-NOV-2006
> DEFINITION  Cryptosporidium environmental sequence clone JF#1 18S  
> small subunit
>             ribosomal RNA gene, partial sequence.
> ACCESSION   EF060289
> VERSION     EF060289.1  GI:117671303
> KEYWORDS    ENV.
> SOURCE      Cryptosporidium environmental sequence
>   ORGANISM  Cryptosporidium environmental sequence
>             Eukaryota; Alveolata; Apicomplexa; Coccidia;  
> Eucoccidiorida;
>             Eimeriorina; Cryptosporidiidae; Cryptosporidium;  
> environmental
>             samples.
> REFERENCE   1  (bases 1 to 425)
>   AUTHORS   Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Phylogenetic analysis implicates birds as an important  
> source of
>             Cryptosporidium spp. oocysts in agricultural watersheds
>   JOURNAL   Unpublished
> REFERENCE   2  (bases 1 to 425)
>   AUTHORS   Jellison,K.L.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (12-OCT-2006) Civil and Environmental  
> Engineering, Lehigh
>             University, Fritz Engineering Laboratory, 13 E. Packer  
> Avenue,
>             Bethlehem, PA 18015, USA
> FEATURES             Location/Qualifiers
>      source          1..425
>                      /organism="Cryptosporidium environmental  
> sequence"
>                      /mol_type="genomic DNA"
>                      /isolation_source="environmental water sample"
>                      /db_xref="taxon:310753"
>                      /clone="JF#1"
>                      /environmental_sample
>                      /country="USA: Massachusetts"
>                      /collection_date="Jun-2001"
>                      /collected_by="Kristen Jellison"
>                      /PCR_primers="fwd_name: CPB-DIAGF, rev_name:  
> CPB-DIAGR"
>      rRNA            <1..>425
>                      /product="18S small subunit ribosomal RNA"
> ORIGIN
>         1 aagctcgtag ttggatttct gctaatattc tatgtaaatg cttttgcctt  
> tacatgttgt
>        61 tagccttccc cgtattactg cttcagtatg cggattttac tttgagaaaa  
> ttagagtgct
>       121 taaagcaggc ttttgccttg aatactccag catggaataa tattaaagat  
> ttttatcttt
>       181 cttattggtt ctaagataaa aataatgatt aatagggaca gttgggggca  
> tttgtattta
>       241 acagtcagag gtgaaattct tagatttgtt aaagacaaac tagtgcgaaa  
> gcatttgcca
>       301 aggatgtttt cattaatcaa gaacgaaagt taggggatcg aagacgatca  
> gataccgtcg
>       361 tagtcttaac cataaactat gccaactaga gattggaggt tgttccttac  
> tccttcagca
>       421 cctta
> //
> LOCUS       EF060290                 425 bp    DNA     linear   ENV  
> 14-NOV-2006
> DEFINITION  Cryptosporidium environmental sequence clone JF#2 18S  
> small subunit
>             ribosomal RNA gene, partial sequence.
> ACCESSION   EF060290
> VERSION     EF060290.1  GI:117671304
> KEYWORDS    ENV.
> SOURCE      Cryptosporidium environmental sequence
>   ORGANISM  Cryptosporidium environmental sequence
>             Eukaryota; Alveolata; Apicomplexa; Coccidia;  
> Eucoccidiorida;
>             Eimeriorina; Cryptosporidiidae; Cryptosporidium;  
> environmental
>             samples.
> REFERENCE   1  (bases 1 to 425)
>   AUTHORS   Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Phylogenetic analysis implicates birds as an important  
> source of
>             Cryptosporidium spp. oocysts in agricultural watersheds
>   JOURNAL   Unpublished
> REFERENCE   2  (bases 1 to 425)
>   AUTHORS   Jellison,K.L.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (12-OCT-2006) Civil and Environmental  
> Engineering, Lehigh
>             University, Fritz Engineering Laboratory, 13 E. Packer  
> Avenue,
>             Bethlehem, PA 18015, USA
> FEATURES             Location/Qualifiers
>      source          1..425
>                      /organism="Cryptosporidium environmental  
> sequence"
>                      /mol_type="genomic DNA"
>                      /isolation_source="environmental water sample"
>                      /db_xref="taxon:310753"
>                      /clone="JF#2"
>                      /environmental_sample
>                      /country="USA: Massachusetts"
>                      /collection_date="Jun-2001"
>                      /collected_by="Kristen Jellison"
>                      /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name:
>                      CPB-DIAGR"
>      rRNA            <1..>425
>                      /product="18S small subunit ribosomal RNA"
> ORIGIN
>         1 aagctcgtag ttggatttct gctaatattc tatgtaaatg cttttgcctt  
> tacatgttgt
>        61 tagccttccc cgtattactg cttcagtatg cggattttac tttgagaaaa  
> ttagagtgct
>       121 taaagcaggc tcttgccttg aatactccag catggaataa taccaaggat  
> ttttgtcctt
>       181 cttattggtt ctaggataga aataatgatt aatagggaca gttgggggca  
> tttgtattta
>       241 acagccagag gtgaaattct tagacttgtt aaagacaaac tagtgcgaaa  
> gcatttgcca
>       301 aggatgtttt cattaatcaa gaacgaaagt taggggatcg aagacgatca  
> gataccgtcg
>       361 tagtcttaac cataaactat gccaactaga gattggaggt tgttccttac  
> tccttcagca
>       421 cctta
> //
> LOCUS       EF060291                 429 bp    DNA     linear   ENV  
> 14-NOV-2006
> DEFINITION  Cryptosporidium environmental sequence clone JF#3 18S  
> small subunit
>             ribosomal RNA gene, partial sequence.
> ACCESSION   EF060291
> VERSION     EF060291.1  GI:117671305
> KEYWORDS    ENV.
> SOURCE      Cryptosporidium environmental sequence
>   ORGANISM  Cryptosporidium environmental sequence
>             Eukaryota; Alveolata; Apicomplexa; Coccidia;  
> Eucoccidiorida;
>             Eimeriorina; Cryptosporidiidae; Cryptosporidium;  
> environmental
>             samples.
> REFERENCE   1  (bases 1 to 429)
>   AUTHORS   Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Phylogenetic analysis implicates birds as an important  
> source of
>             Cryptosporidium spp. oocysts in agricultural watersheds
>   JOURNAL   Unpublished
> REFERENCE   2  (bases 1 to 429)
>   AUTHORS   Jellison,K.L.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (12-OCT-2006) Civil and Environmental  
> Engineering, Lehigh
>             University, Fritz Engineering Laboratory, 13 E. Packer  
> Avenue,
>             Bethlehem, PA 18015, USA
> FEATURES             Location/Qualifiers
>      source          1..429
>                      /organism="Cryptosporidium environmental  
> sequence"
>                      /mol_type="genomic DNA"
>                      /isolation_source="environmental water sample"
>                      /db_xref="taxon:310753"
>                      /clone="JF#3"
>                      /environmental_sample
>                      /country="USA: Massachusetts"
>                      /collection_date="Aug-2001"
>                      /collected_by="Kristen Jellison"
>                      /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name:
>                      CPB-DIAGR"
>      rRNA            <1..>429
>                      /product="18S small subunit ribosomal RNA"
> ORIGIN
>         1 aagctcgtag ttggatttct gttagtgtct tatatcttgt actttattgt  
> acttgtatag
>        61 tactaacata attcatatta ctttttagta ttatgaaatt ttactttgag  
> aaaattagag
>       121 tgcttaaagc aggcttttgc cttgaatact ccagcatgga ataatacgaa  
> ggatttttat
>       181 ctttcttatt ggttctaaga taaaaataat ggttaatagg aacagttggg  
> ggcatttgta
>       241 tttaacagtc agaggtgaaa ttcttagatt tgttaaagac aaactaatgc  
> gaaagcattt
>       301 gccaaggatg ttttcattaa tcaagaacga aagttagggg atcgaagacg  
> atcagatacc
>       361 gtcgtagtct taaccataaa ctatgccaac tagagattgg aggttgttcc  
> ttactccttc
>       421 agcacctta
> //
> LOCUS       EF060292                 430 bp    DNA     linear   ENV  
> 14-NOV-2006
> DEFINITION  Cryptosporidium environmental sequence clone JF#4 18S  
> small subunit
>             ribosomal RNA gene, partial sequence.
> ACCESSION   EF060292
> VERSION     EF060292.1  GI:117671306
> KEYWORDS    ENV.
> SOURCE      Cryptosporidium environmental sequence
>   ORGANISM  Cryptosporidium environmental sequence
>             Eukaryota; Alveolata; Apicomplexa; Coccidia;  
> Eucoccidiorida;
>             Eimeriorina; Cryptosporidiidae; Cryptosporidium;  
> environmental
>             samples.
> REFERENCE   1  (bases 1 to 430)
>   AUTHORS   Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Phylogenetic analysis implicates birds as an important  
> source of
>             Cryptosporidium spp. oocysts in agricultural watersheds
>   JOURNAL   Unpublished
> REFERENCE   2  (bases 1 to 430)
>   AUTHORS   Jellison,K.L.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (12-OCT-2006) Civil and Environmental  
> Engineering, Lehigh
>             University, Fritz Engineering Laboratory, 13 E. Packer  
> Avenue,
>             Bethlehem, PA 18015, USA
> FEATURES             Location/Qualifiers
>      source          1..430
>                      /organism="Cryptosporidium environmental  
> sequence"
>                      /mol_type="genomic DNA"
>                      /isolation_source="environmental water sample"
>                      /db_xref="taxon:310753"
>                      /clone="JF#4"
>                      /environmental_sample
>                      /country="USA: Massachusetts"
>                      /collection_date="Nov-2001"
>                      /collected_by="Kristen Jellison"
>                      /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name:
>                      CPB-DIAGR"
>      rRNA            <1..>430
>                      /product="18S small subunit ribosomal RNA"
> ORIGIN
>         1 aagctcgtag ttggatttct gttaattgtt tatatgattt atcttataat  
> atttatatag
>        61 cattaacata attcatatta ctatttttag tatatgaaat tttactttga  
> gaaaattaga
>       121 gtgcttaaag caggcttttg ccttgaatac tccagcatgg aataatatta  
> aagattttta
>       181 tctttcttat tggttctaag atagaaataa tgattaatag ggacagttgg  
> gggcatttgt
>       241 atttaacagt cagaggtgaa attcttagat ttgttaaaga caaactagtg  
> cgaaagcatt
>       301 tgccaaggat gttttcatta atcaagaacg aaagttaggg gatcgaagac  
> gatcagatac
>       361 cgtcgtagac ttaaccataa actatgccaa ctagagattg gaggttgttc  
> cttactcctt
>       421 cagcacctta
> //
> LOCUS       EF060293                 432 bp    DNA     linear   ENV  
> 14-NOV-2006
> DEFINITION  Cryptosporidium environmental sequence clone JF#5 18S  
> small subunit
>             ribosomal RNA gene, partial sequence.
> ACCESSION   EF060293
> VERSION     EF060293.1  GI:117671307
> KEYWORDS    ENV.
> SOURCE      Cryptosporidium environmental sequence
>   ORGANISM  Cryptosporidium environmental sequence
>             Eukaryota; Alveolata; Apicomplexa; Coccidia;  
> Eucoccidiorida;
>             Eimeriorina; Cryptosporidiidae; Cryptosporidium;  
> environmental
>             samples.
> REFERENCE   1  (bases 1 to 432)
>   AUTHORS   Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Phylogenetic analysis implicates birds as an important  
> source of
>             Cryptosporidium spp. oocysts in agricultural watersheds
>   JOURNAL   Unpublished
> REFERENCE   2  (bases 1 to 432)
>   AUTHORS   Jellison,K.L.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (12-OCT-2006) Civil and Environmental  
> Engineering, Lehigh
>             University, Fritz Engineering Laboratory, 13 E. Packer  
> Avenue,
>             Bethlehem, PA 18015, USA
> FEATURES             Location/Qualifiers
>      source          1..432
>                      /organism="Cryptosporidium environmental  
> sequence"
>                      /mol_type="genomic DNA"
>                      /isolation_source="environmental water sample"
>                      /db_xref="taxon:310753"
>                      /clone="JF#5"
>                      /environmental_sample
>                      /country="USA: Massachusetts"
>                      /collection_date="Nov-2001"
>                      /collected_by="Kristen Jellison"
>                      /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name:
>                      CPB-DIAGR"
>      rRNA            <1..>432
>                      /product="18S small subunit ribosomal RNA"
> ORIGIN
>         1 aagctcgtag ttggatttct gttaattgtt tatatttgtt atctattgat  
> acttgtataa
>        61 cactaacata attcatatta ctatttatct agtatatgaa agtttacttt  
> gagaaaatta
>       121 gagtgcttaa agcaggcttt tgccttgaat actccaacat ggaataatat  
> aaaagatttt
>       181 tatctttctt attggttcta agatagaaat aatgattaat agggacagtt  
> gggggcattt
>       241 gtatttaaca gtcagaggtg aaattcttag atttgttaaa gacaaactag  
> tgcgaaagca
>       301 tttgccaagg atgttttcat taatcaagaa cgaaagttag gggatcgaag  
> acgatcagat
>       361 accgccgtag tcttaaccat aaactatgcc aactagagat tggaggttgt  
> tccttactcc
>       421 ttcagcacct ta
> //
> LOCUS       EF060294                 432 bp    DNA     linear   ENV  
> 14-NOV-2006
> DEFINITION  Cryptosporidium environmental sequence clone JF#6 18S  
> small subunit
>             ribosomal RNA gene, partial sequence.
> ACCESSION   EF060294
> VERSION     EF060294.1  GI:117671308
> KEYWORDS    ENV.
> SOURCE      Cryptosporidium environmental sequence
>   ORGANISM  Cryptosporidium environmental sequence
>             Eukaryota; Alveolata; Apicomplexa; Coccidia;  
> Eucoccidiorida;
>             Eimeriorina; Cryptosporidiidae; Cryptosporidium;  
> environmental
>             samples.
> REFERENCE   1  (bases 1 to 432)
>   AUTHORS   Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Phylogenetic analysis implicates birds as an important  
> source of
>             Cryptosporidium spp. oocysts in agricultural watersheds
>   JOURNAL   Unpublished
> REFERENCE   2  (bases 1 to 432)
>   AUTHORS   Jellison,K.L.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (12-OCT-2006) Civil and Environmental  
> Engineering, Lehigh
>             University, Fritz Engineering Laboratory, 13 E. Packer  
> Avenue,
>             Bethlehem, PA 18015, USA
> FEATURES             Location/Qualifiers
>      source          1..432
>                      /organism="Cryptosporidium environmental  
> sequence"
>                      /mol_type="genomic DNA"
>                      /isolation_source="environmental water sample"
>                      /db_xref="taxon:310753"
>                      /clone="JF#6"
>                      /environmental_sample
>                      /country="USA: Massachusetts"
>                      /collection_date="Nov-2001"
>                      /collected_by="Kristen Jellison"
>                      /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name:
>                      CPB-DIAGR"
>      rRNA            <1..>432
>                      /product="18S small subunit ribosomal RNA"
> ORIGIN
>         1 aagctcgtag ttggatttct gttaattgtt tatatttgtt atctattgat  
> acttgtataa
>        61 cattaacata attcatatta ctatttatct agtatatgaa attttacttt  
> gagaaaatta
>       121 gagtgcttaa agcaggcttt tgccttgaat actccagcat ggaataatat  
> taaagatttt
>       181 tatcattctt attggttcta agatagaaat aatgattaat agggacagtt  
> gggggcattt
>       241 gtatttaaca gtcagaggtg aaattcttag atttgttaaa gacaaactag  
> tgcgaaagca
>       301 tttgccaagg atgttttcat taatcaagaa cgaaagttag gggatcgaag  
> acgatcagat
>       361 accgtcgtag tcataaccat aaactatgcc aactagagat tggaggttgt  
> tccttactcc
>       421 ttcagcacct ta
> //
> LOCUS       EF060295                 425 bp    DNA     linear   ENV  
> 14-NOV-2006
> DEFINITION  Cryptosporidium environmental sequence clone Cow 18S  
> small subunit
>             ribosomal RNA gene, partial sequence.
> ACCESSION   EF060295
> VERSION     EF060295.1  GI:117671309
> KEYWORDS    ENV.
> SOURCE      Cryptosporidium environmental sequence
>   ORGANISM  Cryptosporidium environmental sequence
>             Eukaryota; Alveolata; Apicomplexa; Coccidia;  
> Eucoccidiorida;
>             Eimeriorina; Cryptosporidiidae; Cryptosporidium;  
> environmental
>             samples.
> REFERENCE   1  (bases 1 to 425)
>   AUTHORS   Jellison,K.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Sources and species of Cryptosporidium oocysts in the  
> Wachusett
>             Reservoir watershed
>   JOURNAL   Appl. Environ. Microbiol. 68 (2), 569-575 (2002)
>    PUBMED   11823192
> REFERENCE   2  (bases 1 to 425)
>   AUTHORS   Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Phylogenetic analysis implicates birds as an important  
> source of
>             Cryptosporidium spp. oocysts in agricultural watersheds
>   JOURNAL   Unpublished
> REFERENCE   3  (bases 1 to 425)
>   AUTHORS   Jellison,K.L., Distel,D.L. and Hemond,H.F.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (12-OCT-2006) Civil and Environmental  
> Engineering, Lehigh
>             University, Fritz Engineering Laboratory, 13 E. Packer  
> Avenue,
>             Bethlehem, PA 18015, United States
> FEATURES             Location/Qualifiers
>      source          1..425
>                      /organism="Cryptosporidium environmental  
> sequence"
>                      /mol_type="genomic DNA"
>                      /isolation_source="adult Bos taurus"
>                      /db_xref="taxon:310753"
>                      /clone="Cow"
>                      /environmental_sample
>                      /country="USA: Massachusetts"
>                      /collection_date="Jun-2000"
>                      /collected_by="Kristen Jellison"
>                      /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name:
>                      CPB-DIAGR"
>      rRNA            <1..>425
>                      /product="18S small subunit ribosomal RNA"
> ORIGIN
>         1 aagctcgtag ttggatttct gttaattttt atatataata tcacgatatt  
> tatataatat
>        61 taacataatt catattactt tttagtatat gaaactttac tttgagaaaa  
> ttagagtgct
>       121 taaagcaggc tattgccttg aatactccag catggaataa tattaaggat  
> ttttattctt
>       181 cttattggtt ctagaataaa aatgatgatt aatagggaca gttgggggca  
> tttgtattta
>       241 acagtcagag gtgaaattct tagatttgtt aaagacaaac tactgcgaaa  
> gcatttgcca
>       301 aggatgtttt cattaatcaa gaacgaaagt taggggatcg aagacgatca  
> gataccgtcg
>       361 tagtcttaac cattaactat gccaactaga gattggaggt tgttccttac  
> tccttcagca
>       421 cctta
> //
> LOCUS       EF060296                 431 bp    DNA     linear   ENV  
> 14-NOV-2006
> DEFINITION  Cryptosporidium environmental sequence clone Manure 18S  
> small
>             subunit ribosomal RNA gene, partial sequence.
> ACCESSION   EF060296
> VERSION     EF060296.1  GI:117671310
> KEYWORDS    ENV.
> SOURCE      Cryptosporidium environmental sequence
>   ORGANISM  Cryptosporidium environmental sequence
>             Eukaryota; Alveolata; Apicomplexa; Coccidia;  
> Eucoccidiorida;
>             Eimeriorina; Cryptosporidiidae; Cryptosporidium;  
> environmental
>             samples.
> REFERENCE   1  (bases 1 to 431)
>   AUTHORS   Jellison,K.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Sources and species of Cryptosporidium oocysts in the  
> Wachusett
>             Reservoir watershed
>   JOURNAL   Appl. Environ. Microbiol. 68 (2), 569-575 (2002)
>    PUBMED   11823192
> REFERENCE   2  (bases 1 to 431)
>   AUTHORS   Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Phylogenetic analysis implicates birds as an important  
> source of
>             Cryptosporidium spp. oocysts in agricultural watersheds
>   JOURNAL   Unpublished
> REFERENCE   3  (bases 1 to 431)
>   AUTHORS   Jellison,K.L.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (12-OCT-2006) Civil and Environmental  
> Engineering, Lehigh
>             University, Fritz Engineering Laboratory, 13 E. Packer  
> Avenue,
>             Bethlehem, PA 18015, USA
> FEATURES             Location/Qualifiers
>      source          1..431
>                      /organism="Cryptosporidium environmental  
> sequence"
>                      /mol_type="genomic DNA"
>                      /isolation_source="farm manure pit"
>                      /db_xref="taxon:310753"
>                      /clone="Manure"
>                      /environmental_sample
>                      /country="USA: Massachusetts"
>                      /collection_date="Jun-2000"
>                      /collected_by="Kristen Jellison"
>                      /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name:
>                      CPB-DIAGR"
>      rRNA            <1..>431
>                      /product="18S small subunit ribosomal RNA"
> ORIGIN
>         1 aagctcgtag ttggatttct gttgtataat ttataatatt accaaggtaa  
> ttattatatt
>        61 atcaacatcc ttcctattat attctaaata tataggaaat tttactttga  
> gaaaattaga
>       121 gtgcttaaag caggcaactg ccttgaatac tccagcatgg aataataagt  
> aaggactttt
>       181 gtctttctta ttggttctag gacaaaagta atggttaata gggacagttg  
> ggggcattcg
>       241 tatttaacag ccagaggtga aattcttaga tttgttaaag acgaactact  
> gcgaaagcat
>       301 ttgccaagga tgttttcatt aatcaagaac gaaagttagg ggatcgaaga  
> cgatcagata
>       361 ccgtcgtagt cttaaccata aactatgccg actagagatt ggaggttgtt  
> ccttactcct
>       421 tcagcacctt a
> //
> LOCUS       EF060297                 431 bp    DNA     linear   ENV  
> 14-NOV-2006
> DEFINITION  Cryptosporidium environmental sequence clone SF 18S  
> small subunit
>             ribosomal RNA gene, partial sequence.
> ACCESSION   EF060297
> VERSION     EF060297.1  GI:117671311
> KEYWORDS    ENV.
> SOURCE      Cryptosporidium environmental sequence
>   ORGANISM  Cryptosporidium environmental sequence
>             Eukaryota; Alveolata; Apicomplexa; Coccidia;  
> Eucoccidiorida;
>             Eimeriorina; Cryptosporidiidae; Cryptosporidium;  
> environmental
>             samples.
> REFERENCE   1  (bases 1 to 431)
>   AUTHORS   Jellison,K.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Sources and species of Cryptosporidium oocysts in the  
> Wachusett
>             Reservoir watershed
>   JOURNAL   Appl. Environ. Microbiol. 68 (2), 569-575 (2002)
>    PUBMED   11823192
> REFERENCE   2  (bases 1 to 431)
>   AUTHORS   Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B.
>   TITLE     Phylogenetic analysis implicates birds as an important  
> source of
>             Cryptosporidium spp. oocysts in agricultural watersheds
>   JOURNAL   Unpublished
> REFERENCE   3  (bases 1 to 431)
>   AUTHORS   Jellison,K.L.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (12-OCT-2006) Civil and Environmental  
> Engineering, Lehigh
>             University, Fritz Engineering Laboratory, 13 E. Packer  
> Avenue,
>             Bethlehem, PA 18015, USA
> FEATURES             Location/Qualifiers
>      source          1..431
>                      /organism="Cryptosporidium environmental  
> sequence"
>                      /mol_type="genomic DNA"
>                      /isolation_source="environmental water sample"
>                      /db_xref="taxon:310753"
>                      /clone="SF"
>                      /environmental_sample
>                      /country="USA: Massachusetts"
>                      /collection_date="Mar-1999"
>                      /collected_by="Kristen Jellison"
>                      /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name:
>                      CPB-DIAGR"
>      rRNA            <1..>431
>                      /product="18S small subunit ribosomal RNA"
> ORIGIN
>         1 aagctcgtag ttggatttct gctgtataat ttataatatt accaaggtaa  
> ttattatatt
>        61 atcaacatcc ttcctattat attctaaata tataggaaat tttactttga  
> gaaaattaga
>       121 gtgcttaaag caggcaactg ccttgaatac tccagcatgg aataataagt  
> aaggactttt
>       181 gtctttctta ttggttctag gacaaaagta atggttaata gggacagttg  
> ggggcattcg
>       241 tatttaacag ccagaggtga agttcttaga tttgttaaag acgaactact  
> gcgaaagcat
>       301 ttgccaagga tgttttcatt aatcaagaac gaaagttagg ggatcgaaga  
> cgatcagata
>       361 ccgtcgtagt cttaaccata aactatgccg actagagatt ggaggttgtt  
> ccttactcct
>       421 tcagcacctt a
> //
>
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