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| | == WormBase Genomes == | | == WormBase Genomes == |
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| − | This is a record of the current and proposed set of genomes in WormBase.
| + | An up to date list of genomes in WormBase can be found at: http://www.wormbase.org/species/all |
| − | | |
| − | I think that this page is a correct statement of our intentions.
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| − | | |
| − | We may, of course, alter our plans for which species to include as circumstances dictate and so the list of organisms which should be included should be treated as somewhat tentative.
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| − | | |
| − | | |
| − | === Tiers ===
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| − | | |
| − | The different genomes in WormBase are classified in various tiers which depend on the amount of curation effort we are able to put into maintaining them.
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| − | | |
| − | '''Tier I''' - All efforts are made to curate the gene structures and any other genetic or metabolic information. Only '''C. elegans''' is in this group.
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| − | | |
| − | '''Tier II''' - Efforts are made, where practical, to manually curate the gene structure and possibly some other genomic information. WormBase 'owns' the assembly in the [http://www.ebi.ac.uk/ena/ ENA] and GenBank so that new gene annotations can be submitted to the ENA/GenBank by WormBase.
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| − | | |
| − | '''Tier III''' - We will set up the genome on WormBase with any gene structures that the authors of this genome have predicted. No further curation efforts are made by the WormBase consortium.
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| − | | |
| − | '''Tier IV''' - Proposed tier for organisms with only transcriptome information and no coherent genome. There are no examples of this in WormBase at present.
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| − | | |
| − | '''Tier V''' - Proposed tier for organisms with only genome information and no coherent transcriptome. There are no examples of this in WormBase at present.
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| − | | |
| − | === Genome ===
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| − | | |
| − | The '''Genome''' column in the table indicates whether the genome has been added to WormBase.
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| − | | |
| − | === Gene ===
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| − | | |
| − | The '''Genes''' column in the table indicates whether gene structures have been added to WormBase.
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| − | | |
| − | === The genome status ===
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| − | | |
| − | {| class="wikitable" border="1"
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| − | |-
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| − | ! Species
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| − | ! NCBI TaxonID
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| − | ! Tier
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| − | ! Genome
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| − | ! Genes
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| − | ! Origin
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| − | ! Comments
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| − | |-
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| − | | [[Caenorhabditis briggsae|''Caenorhabditis briggsae'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6238 6238]
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| − | | II
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/c_briggsae/ Yes]
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| − | | Yes
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| − | | WashU
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| − | | [Sept 2010] New assembly from Erich Haag being worked on.
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| − | |-
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| − | | [[Caenorhabditis remanei|''Caenorhabditis remanei'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=31234 31234]
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| − | | II
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/c_remanei/ Yes]
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| − | | Yes
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| − | | WashU
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| − | |
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| − | |-
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| − | | [[Caenorhabditis brenneri|''Caenorhabditis brenneri'']]<br>(Species 4)
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=135651 135651]
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| − | | II
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/c_brenneri/ Yes]
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| − | | Yes
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| − | | WashU
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| − | | [Jan 2011] The current assembly contains quite a bit of heterozygosity
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| − | |-bgcolor="#00D7D7"
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| − | | [[Caenorhabditis elegans|''Caenorhabditis elegans strain N2'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
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| − | | I
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/c_elegans/ Yes]
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| − | | Yes
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| − | | WashU/Sanger
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| − | |
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| − | |-
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| − | | Caenorhabditis elegans strain DR1035
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
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| − | | III
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| − | |
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| − | |
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| − | | Mark Blaxter
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| − | | status unclear
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| − | |-
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| − | | [[Caenorhabditis japonica|''Caenorhabditis japonica'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=281687 281687]
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| − | | II
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/c_japonica/ Yes]
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| − | | Yes
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| − | | WashU
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| − | | [Jan 2011] New/improved assembly is being worked on at WashU
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| − | |-
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| − | | Caenorhabditis drosophilae
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96641 96641]
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| − | | III
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| − | |
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| − | |
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| − | | WashU
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| − | | [Sept 2010] being assembled
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| − | |-
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| − | | [[Caenorhabditis angaria|''Caenorhabditis angaria'']] (species 3 strain PS1010)
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96668 96668]
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| − | | III
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| − | | Yes
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| − | | Yes
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| − | | CalTech
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| − | | Added to WormBase in release WS218.<br>[Jan 2011] This species now has an official name of '''C. angaria'''
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| − | |-
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| − | | Caenorhabditis species 7 strain JU1286
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870436 870436]
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| − | | V
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| − | |
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| − | |
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| − | | WashU
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| − | | released in WS226
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| − | |-
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| − | | Caenorhabditis species 9 strain JU1422
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870437 870437]
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| − | | V
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| − | |
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| − | |
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| − | | WashU
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| − | | released in WS226
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| − | |-
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| − | | Caenorhabditis species 11 strain JU1373
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=886184 886184]
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| − | | V
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| − | |
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| − | |
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| − | | WashU
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| − | | released in WS226
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| − | |-
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| − | | [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=37862 37862]
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| − | | V
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| − | |
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| − | |
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| − | | WashU
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| − | | Jan 2011 - Submitted to GenBank - Accession: EF043402 Annotation is being done. Sep 2011 - Will be in WormBase soon.
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| − | |-
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| − | | [[Pristionchus pacificus|''Pristionchus pacificus'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=54126 54126]
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| − | | II
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/p_pacificus/ Yes]
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| − | | Yes
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| − | | WashU/MPI
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| − | | [16 December 2010] Updated to the newest assembly and geneset in WS221
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| − | |-
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| − | | [[Haemonchus contortus|''Haemonchus contortus'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6289 6289]
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| − | | III
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/h_contortus/ Yes]
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| − | | Yes
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| − | | Sanger
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| − | | Added to WormBase in release WS209.
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| − | |-
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| − | | [[Strongyloides ratti|''Strongyloides ratti'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34506 34506]
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | | [Jan 2011] draft assembly in GenBank, released in WS226
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| − | |-
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| − | | [[Meloidogyne hapla|''Meloidogyne hapla'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6305 6305]
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| − | | III
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/m_hapla/ Yes]
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| − | | Yes
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| − | | NCSU hapla.org
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| − | | Added to WormBase in release WS204.
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| − | |-
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| − | | [[Meloidogyne incognita|''Meloidogyne incognita'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6306 6306]
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| − | | III
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/m_incognita/ Yes]
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| − | |
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| − | | INRA
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| − | | Added to WormBase in release WS205. Genes are not yet available.
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| − | |-
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| − | | [[Brugia malayi|''Brugia malayi'']]
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6279 6279]
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| − | | III
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| − | | [http://www.wormbase.org/db/gb2/gbrowse/b_malayi/ Yes]
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| − | | Yes
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| − | | TIGR -> WashU/Sanger
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| − | | [Sept 2010] Currently using the old TIGR assembly. Waiting for WashU (did assembly) and Sanger (did gene models) to publish, then we will use the new assembly.<br>[Dec 2010] merged Augustus gene predictions from Erich Schwarz into WS216
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| − | |-
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| − | | Onchocerca volvulus
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Ascaris suum
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6253 6253]
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Globodera pallida
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=36090 36090]
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Nippostrongylus brasiliensis
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=27835 27835]
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Strongyloides ransomi
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=553534 553534]
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Teladorsagia circumcincta
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=45464 45464]
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Trichuris muris
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=70415 70415]
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Trichinella spiralis
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6334 6334]
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| − | | III
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| − | |
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| − | |
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| − | | WashU
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| − | | [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] will be in WS225
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| − | |-
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| − | | Steinernema carpocapsae
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| − | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34508 34508]
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| − | |
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| − | |
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| − | |
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| − | | Laboratorio Nacional de Genómica para la Biodiversidad / CalTech
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| − | | [May 2011] Being assembled.
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| − | |}
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| − | | |
| − | == Phylogeny ==
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| − | | |
| − | Given my understanding of the current phylogenetic literature (and based on personal communications with [http://www.wormbase.org/db/misc/person?name=WBPerson2076;class=Person Karin Kiontke]), the correct guide tree would be:
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| − | <pre>
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| − | ((((((((C.elegans,(((C.briggsae, C.sp9), C.remanei),(C.sp11, C.brenneri))),(C.sp7, C.japonica)), C.angaria), (H.contortus,H.bacteriophora)), P.pacificus),((M.incognita, M.hapla), S.ratti)), B.malayi), T.spiralis);
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| − | </pre>
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| − | [[File:treeprint2.png]]
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| | == See also == | | == See also == |
