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Teaching

See all Fall Quarter Oceanography Classes

 

In the 2008-09 Academic year Gabrielle will teach Ocean 430 Autumn quarter

 

ASAFind

ASAFind Logo

ASAFind identifies nuclear-encoded plastid proteins in algae with secondary plastids of the red lineage based on the output of SignalP and the identification of conserved “ASAFAP”-motifs and transit peptides. A downloadable stand-alone version can be found at https://bitbucket.org/rocaplab/asafind

Inputs

Takes a Fasta and companion SignalP file (versions 3.0, 4.0 or 4.1) short format file as input, either with the complete SignalP header (two lines starting with ‘#’) or just with the results (first line starts with first sequence name). This tool was developed using 3.0, which remains the recommended version for algae with secondary plastids of the red lineage . Here is a example fasta input and a example signalp input

Sequence Names

SignalP truncates the sequence names to 20 characters. Therefore, ASAFind only considers the first 20 charcacters of the fasta name, which must be unique within the file. Parts of the fasta name after the 20th character are ignored. Additionally, the fasta name may not contain - or | because SignalP changes them to _. If you discover any other characters that SignalP silently changes, please let us know

Minimium Sequence Lengths

ASAFind requires at least 7 aa upstream and 22 aa downstream of the cleavage site identified by SignalP, no prediction is possible for sequences not meeting these requirements.

Output

The output of ASAFind is a tab delimited table, with a prediction for each protein.

Input Fasta:
Enter sequences below in FASTA format
Each sequence name must be unique within first 20 characters.

Or upload a fasta file:

Input companion SignalP data:
Enter output from SignalP in short format (you may omit column headers or leave them in)

Or upload a SignalP output file:

Output
Standard Format
Short Format


Ready?


Portable Version
Would you like to run ASAFind locally? Download a stand alone version of this tool.

Citation

If you use ASAFind in your research please cite our publication Gruber et al., doi: 10.1111/tpj.12734 as well as the publications for the appropriate SignalP versions (Petersen et al., doi: 10.1038/nmeth.1701 for SignalP 4.1 or Bendtsen et al., doi: 10.1016/j.jmb.2004.05.028 for SignalP 3.0).




NSF logo

Support for the development of ASAFind provided by the National Science Foundation, the Gordon and Betty Moore Foundation and the German Research Foundation.

Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the funders.

Home

 

The Thompson

Welcome to the Rocap lab, located in the School of Oceanography at the University of Washington. We study the evolution and ecology of marine bacteria and phytoplankton. We study habitats as close as Puget Sound and as far afield as the South Atlantic Ocean. The multiple projects in the lab all address common questions: How does genetic diversity arise in marine microbial populations, how is it maintained, and how does it influence ecological success.

Our lab is part of the Center for Environmental Genomics, occupying 11,000 square feet of newly renovated lab space in the Benjamin Hall Interdisciplinary Research Building.

MCL clustering for *Base

 

Docs PDF attached below.

Start with all gb files from a *Base in a dir called "genomes".
Convert them all to fasta:
dir_loop.py -c 'genbank_to_fasta.py -q locus_tag -i' -d ./

Cat them into one file:
cat *.fasta > ../features.fasta 

 

Search and replace to remove all "_" endings to sequences. I think these are translations of stop conds?
Search and replace all "GI:" with "GI_".

create_blast_databases.py -f features.fasta -o ./ -F -p

Reciprocal Blast:
blastp -query features.fasta -db features_aa -out features.blast -outfmt 6 -num_threads 4

cut -f 1,2,11 features.blast > features.abc

Process and prepare data for mcl. Transform evalues to more useful metric.
mcxload -abc features.abc -write-tab features.dict -o features.mci --stream-mirror --stream-neg-log10 -stream-tf 'ceil(200)' 

mcl features.mci -I 1.4 && mcl features.mci -I 2 && mcl features.mci -I 6 && mcl features.mci -I 1.2

For each of the 4 outfiles:
mcxdump -icl out.features.mci.I12 -o dump.features.mci.I12 -tabr features.dict

 

If using the dump files for the db, make sure to search and replace "GI_" with "GI:"

May want to make mci files strictly nesting (fine granularity will always conform to course granularity)
clm order -prefix P out.features.mci.I{12,14,20,60}

Make a tree:
clm order -o features.mcltree out.features.mci.I{12,14,20,60}

MitoBase :: Mitochondria Genome Database

There are several ways you can look at the database:

Index of Genomes
This displays all chloroplast genomes publicly available from NCBI

Index of Gene Clusters
This a list of all Gene Clusters.

Index of RNA Clusters
This a list of all RNA Clusters.

About MitoBase
MitoBase technical info and credits.

 

CpBase

Index of Genomes

(337 Genomes)
Organism Locus Sequence Length Assembled Annotated Added
Acidosasa purpurea NC_015820 139697 NA 2011-07-15 2017-01-19
Acorus americanus NC_010093 153819 NA 2011-04-29 2017-01-18
Acorus calamus NC_007407 153821 NA 2009-04-15 2017-01-18
Acutodesmus obliquus NC_008101 161452 NA 2010-03-26 2017-01-19
Adiantum capillus-veneris NC_004766 150568 NA 2010-03-26 2017-01-19
Aethionema cordifolium NC_009265 154168 NA 2010-03-26 2017-01-19
Aethionema grandiflorum NC_009266 154243 NA 2010-03-26 2017-01-19
Ageratina adenophora NC_015621 150698 NA 2012-08-10 2017-01-19
Agrostis stolonifera NC_008591 136584 NA 2011-05-24 2017-01-18
Alsophila spinulosa NC_012818 156661 NA 2011-04-27 2017-01-19
Amborella trichopoda NC_005086 162686 NA 2009-04-15 2017-01-19
Angiopteris evecta NC_008829 153901 NA 2010-03-26 2017-01-18
Anomochloa marantoidea NC_014062 138412 NA 2010-04-23 2017-01-18
Anthoceros formosae NC_004543 161162 NA 2009-04-15 2017-01-19
Anthriscus cerefolium NC_015113 154719 NA 2011-02-10 2017-01-18
Arabidopsis thaliana NC_000932 154478 NA 2010-03-26 2017-01-18
Arabis hirsuta NC_009268 153689 NA 2010-03-26 2017-01-19
Ardisia polysticta NC_021121 156506 NA 2013-05-13 2017-01-19
Artemisia frigida NC_020607 151076 NA 2013-03-25 2017-01-19
Arundinaria gigantea NC_020341 138935 NA 2013-02-25 2017-01-19
Atropa belladonna NC_004561 156687 NA 2010-03-26 2017-01-19
Aureococcus anophagefferens NC_012898 89599 NA 2010-07-02 2017-01-18
Aureoumbra lagunensis NC_012903 94346 NA 2010-07-02 2017-01-19
Bambusa emeiensis NC_015830 139493 NA 2011-07-15 2017-01-19
Bambusa oldhamii NC_012927 139350 NA 2010-03-26 2017-01-19
Barbarea verna NC_009269 154532 NA 2010-03-26 2017-01-19
Bigelowiella natans NC_008408 69166 NA 2010-10-21 2017-01-18
Bismarckia nobilis NC_020366 158210 NA 2013-02-28 2017-01-18
Boea hygrometrica NC_016468 153493 NA 2011-12-20 2017-01-18
Brachypodium distachyon NC_011032 135199 NA 2010-03-26 2017-01-19
Brassica napus NC_016734 152860 NA 2012-04-11 2017-01-19
Bryopsis hypnoides NC_013359 153429 NA 2011-08-01 2017-01-19
Buxus microphylla NC_009599 159010 NA 2009-04-15 2017-01-19
Calamus caryotoides NC_020365 157270 NA 2013-02-28 2017-01-19
Calliarthron tuberculosum NC_021075 178981 NA 2013-05-17 2017-01-19
Calycanthus floridus var. glaucus NC_004993 153337 NA 2009-12-04 2017-01-19
Camellia sinensis NC_020019 157103 NA 2012-12-31 2017-01-18
Capsella bursa-pastoris NC_009270 154490 NA 2010-03-26 2017-01-19
Capsicum annuum NC_018552 156781 NA 2012-09-14 2017-01-19
Carica papaya NC_010323 160100 NA 2010-03-26 2017-01-18
Castanea mollissima NC_014674 160799 NA 2011-01-06 2017-01-19
Catharanthus roseus NC_021423 154950 NA 2013-06-10 2017-01-19
Cathaya argyrophylla NC_014589 107122 NA 2010-10-20 2017-01-19
Cedrus deodara NC_014575 119299 NA 2010-10-20 2017-01-19
Cephalotaxus oliveri NC_021110 134337 NA 2013-05-17 2017-01-18
Cephalotaxus wilsoniana NC_016063 136196 NA 2013-05-17 2017-01-19
Ceratophyllum demersum NC_009962 156252 NA 2009-04-15 2017-01-19
Chaetosphaeridium globosum NC_004115 131183 NA 2009-04-15 2017-01-19
Chara vulgaris NC_008097 184933 NA 2009-04-15 2017-01-18
Cheilanthes lindheimeri NC_014592 155770 NA 2011-02-14 2017-01-19
Chlamydomonas reinhardtii NC_005353 203828 NA 2004-01-23 2017-01-18
Chloranthus spicatus NC_009598 157772 NA 2009-04-15 2017-01-18
Chlorella variabilis NC_015359 124579 NA 2011-04-29 2017-01-18
Chlorella vulgaris NC_001865 150613 NA 2009-04-15 2017-01-19
Chlorokybus atmophyticus NC_008822 152254 NA 2009-04-15 2017-01-19
Chondrus crispus NC_020795 180086 NA 2013-04-05 2017-01-19
Chromera velia NC_014340 120426 NA 2013-05-01 2017-01-19
Chromerida sp. RM11 NC_014345 85535 NA 2010-07-28 2017-01-19
Chrysanthemum indicum NC_020320 150972 NA 2013-02-25 2017-01-19
Chrysanthemum x morifolium NC_020092 151033 NA 2013-01-10 2017-01-18
Cicer arietinum NC_011163 125319 NA 2010-03-26 2017-01-18
Cistanche deserticola NC_021111 102657 NA 2013-05-17 2017-01-18
Citrus sinensis NC_008334 160129 NA 2009-04-15 2017-01-19
Coccomyxa subellipsoidea C-169 NC_015084 175731 NA 2011-02-10 2017-01-18
Coffea arabica NC_008535 155189 NA 2010-03-26 2017-01-19
Coix lacryma-jobi NC_013273 140745 NA 2010-03-26 2017-01-19
Colocasia esculenta NC_016753 162424 NA 2013-01-22 2017-01-18
Corynocarpus laevigata NC_014807 159202 NA 2011-01-31 2017-01-19
Crucihimalaya wallichii NC_009271 155199 NA 2010-03-26 2017-01-18
Cryptomeria japonica NC_010548 131810 NA 2010-03-26 2017-01-19
Cryptomonas paramecium NC_013703 77717 NA 2010-08-23 2017-01-19
Cucumis melo subsp. melo NC_015983 156017 NA 2011-09-13 2017-01-19
Cucumis sativus NC_007144 155293 NA 2009-12-01 2017-01-19
Cunninghamia lanceolata NC_021437 135334 NA 2013-06-17 2017-01-19
Cyanidioschyzon merolae strain 10D NC_004799 149987 NA 2009-04-15 2017-01-18
Cyanidium caldarium NC_001840 164921 NA 2009-05-06 2017-01-19
Cyanophora paradoxa NC_001675 135599 NA 2009-04-15 2017-01-18
Cycas revoluta NC_020319 162489 NA 2013-02-25 2017-01-18
Cycas taitungensis NC_009618 163403 NA 2010-03-26 2017-01-18
Cymbidium aloifolium NC_021429 156904 NA 2013-07-03 2017-01-18
Cymbidium mannii NC_021433 155308 NA 2013-07-15 2017-01-18
Cymbidium sinense NC_021430 155548 NA 2013-06-13 2017-01-18
Cymbidium tortisepalum NC_021431 155627 NA 2013-06-17 2017-01-18
Cymbidium tracyanum NC_021432 156286 NA 2013-06-13 2017-01-18
Dasypogon bromeliifolius NC_020367 157858 NA 2013-02-28 2017-01-18
Datura stramonium NC_018117 155871 NA 2012-07-10 2017-01-19
Daucus carota NC_008325 155911 NA 2010-03-26 2017-01-19
Dendrocalamus latiflorus NC_013088 139394 NA 2010-03-26 2017-01-18
Dioscorea elephantipes NC_009601 152609 NA 2009-12-04 2017-01-18
Draba nemorosa NC_009272 153289 NA 2010-03-26 2017-01-18
Drimys granadensis NC_008456 160604 NA 2010-03-26 2017-01-19
Dunaliella salina NC_016732 269044 NA 2012-04-11 2017-01-18
Durinskia baltica NC_014287 116470 NA 2010-06-30 2017-01-18
Ectocarpus siliculosus NC_013498 139954 NA 2009-11-21 2017-01-19
Elaeis guineensis NC_017602 156973 NA 2012-08-09 2017-01-19
Eleutherococcus senticosus NC_016430 156768 NA 2011-12-06 2017-01-18
Elodea canadensis NC_018541 156700 NA 2013-07-10 2017-01-18
Emiliania huxleyi NC_007288 105309 NA 2010-05-03 2017-01-18
Ephedra equisetina NC_011954 109518 NA 2011-10-21 2017-01-18
Equisetum arvense NC_014699 133309 NA 2010-12-02 2017-01-18
Equisetum hyemale NC_020146 131760 NA 2013-01-22 2017-01-18
Erodium carvifolium NC_015083 116935 NA 2011-02-10 2017-01-18
Erodium guttatum NC_018762 128510 NA 2012-10-14 2017-01-19
Erodium texanum NC_014569 130812 NA 2011-01-06 2017-01-18
Eucalyptus globulus subsp. globulus NC_008115 160286 NA 2009-04-15 2017-01-18
Eucalyptus grandis NC_014570 160137 NA 2010-10-21 2017-01-18
Euglena gracilis NC_001603 143171 NA 2010-03-26 2017-01-19
Eutreptiella gymnastica NC_017754 67623 NA 2012-12-11 2017-01-19
Fagopyrum esculentum subsp. ancestrale NC_010776 159599 NA 2010-03-26 2017-01-18
Ferrocalamus rimosivaginus NC_015831 139467 NA 2011-07-15 2017-01-19
Festuca altissima NC_019648 135272 NA 2013-04-10 2017-01-19
Festuca arundinacea NC_011713 136048 NA 2010-08-23 2017-01-19
Festuca ovina NC_019649 133165 NA 2013-04-10 2017-01-18
Festuca pratensis NC_019650 135291 NA 2013-04-10 2017-01-19
Fistulifera sp. JPCC DA0580 NC_015403 134918 NA 2011-04-27 2017-01-19
Floydiella terrestris NC_014346 521168 NA 2010-08-20 2017-01-18
Fragaria chiloensis NC_019601 155603 NA 2013-05-17 2017-01-18
Fragaria mandshurica NC_018767 129805 NA 2012-10-14 2017-01-19
Fragaria vesca subsp. bracteata NC_018766 129788 NA 2012-10-14 2017-01-19
Fragaria vesca subsp. vesca NC_015206 155691 NA 2011-05-12 2017-01-18
Fragaria virginiana NC_019602 155621 NA 2013-05-17 2017-01-19
Francoa sonchifolia NC_021101 157312 NA 2013-05-17 2017-01-19
Fucus vesiculosus NC_016735 124986 NA 2012-02-17 2017-01-19
Geranium palmatum NC_014573 155794 NA 2011-01-06 2017-01-19
Ginkgo biloba NC_016986 156988 NA 2012-03-15 2017-01-19
Glycine max NC_007942 152218 NA 2009-04-15 2017-01-18
Glycine tomentella NC_021636 152728 NA 2013-07-03 2017-01-19
Gnetum montanum NC_021438 115019 NA 2013-06-17 2017-01-19
Gnetum parvifolium NC_011942 114914 NA 2010-03-26 2017-01-18
Gonium pectorale NC_020438 222582 NA 2013-03-07 2017-01-18
Gossypium areysianum NC_018112 159572 NA 2012-07-10 2017-01-18
Gossypium barbadense NC_008641 160317 NA 2010-03-26 2017-01-19
Gossypium capitis-viridis NC_018111 159467 NA 2012-07-10 2017-01-18
Gossypium darwinii NC_016670 160378 NA 2012-09-14 2017-01-18
Gossypium gossypioides NC_017894 159959 NA 2012-09-14 2017-01-19
Gossypium herbaceum subsp. africanum NC_016692 160315 NA 2012-09-14 2017-01-19
Gossypium hirsutum NC_007944 160301 NA 2010-03-26 2017-01-19
Gossypium incanum NC_018109 159205 NA 2012-07-10 2017-01-18
Gossypium mustelinum NC_016711 160313 NA 2012-09-14 2017-01-18
Gossypium raimondii NC_016668 160161 NA 2012-09-14 2017-01-18
Gossypium robinsonii NC_018113 159849 NA 2012-07-10 2017-01-19
Gossypium somalense NC_018110 159539 NA 2012-07-10 2017-01-19
Gossypium thurberi NC_015204 160264 NA 2011-03-04 2017-01-19
Gossypium tomentosum NC_016690 160433 NA 2012-09-14 2017-01-19
Gracilaria tenuistipitata var. liui NC_006137 183883 NA 2009-04-15 2017-01-19
Grateloupia taiwanensis NC_021618 191270 NA 2013-07-02 2017-01-18
Guillardia theta NC_000926 121524 NA 2009-05-06 2017-01-18
Guizotia abyssinica NC_010601 151762 NA 2010-10-21 2017-01-18
Helianthus annuus NC_007977 151104 NA 2009-12-01 2017-01-19
Heliconia collinsiana NC_020362 161907 NA 2013-02-28 2017-01-19
Heterosigma akashiwo NC_010772 159370 NA 2009-05-14 2017-01-19
Hevea brasiliensis NC_015308 161191 NA 2011-03-25 2017-01-18
Hordeum vulgare subsp. vulgare NC_008590 136462 NA 2009-04-15 2017-01-19
Huperzia lucidula NC_006861 154373 NA 2011-03-11 2017-01-19
Illicium oligandrum NC_009600 148553 NA 2009-04-15 2017-01-18
Indocalamus longiauritus NC_015803 139668 NA 2011-07-14 2017-01-19
Ipomoea purpurea NC_009808 162046 NA 2009-12-04 2017-01-19
Isoetes flaccida NC_014675 145303 NA 2010-12-02 2017-01-18
Jacobaea vulgaris NC_015543 150689 NA 2011-06-02 2017-01-19
Jasminum nudiflorum NC_008407 165121 NA 2009-12-04 2017-01-19
Jatropha curcas NC_012224 163856 NA 2010-03-26 2017-01-19
Keteleeria davidiana NC_011930 117720 NA 2010-03-26 2017-01-19
Kryptoperidinium foliaceum NC_014267 140426 NA 2010-06-30 2017-01-18
Lactuca sativa NC_007578 152765 NA 2009-04-15 2017-01-18
Larix decidua NC_016058 122474 NA 2012-08-09 2017-01-19
Lathyrus sativus NC_014063 121020 NA 2010-12-07 2017-01-19
Leersia tisserantii NC_016677 136551 NA 2012-01-27 2017-01-18
Lemna minor NC_010109 165955 NA 2009-04-15 2017-01-19
Lepidium virginicum NC_009273 154743 NA 2009-12-04 2017-01-19
Leptosira terrestris NC_009681 195081 NA 2010-03-26 2017-01-19
Liriodendron tulipifera NC_008326 159886 NA 2010-03-26 2017-01-19
Lobularia maritima NC_009274 152659 NA 2010-03-26 2017-01-18
Lolium multiflorum NC_019651 135175 NA 2013-04-10 2017-01-19
Lolium perenne NC_009950 135282 NA 2012-02-27 2017-01-18
Lotus japonicus NC_002694 150519 NA 2009-04-15 2017-01-18
Magnolia denudata NC_018357 160053 NA 2012-08-10 2017-01-19
Magnolia grandiflora NC_020318 159623 NA 2013-02-25 2017-01-19
Magnolia kwangsiensis NC_015892 159667 NA 2011-09-09 2017-01-19
Magnolia officinalis subsp. biloba NC_020317 160105 NA 2013-03-10 2017-01-18
Manihot esculenta NC_010433 161453 NA 2009-05-07 2017-01-19
Mankyua chejuensis NC_017006 146221 NA 2012-04-11 2017-01-19
Marchantia polymorpha NC_001319 121024 NA 2009-05-06 2017-01-18
Medicago truncatula NC_003119 124033 NA 2009-04-15 2017-01-19
Megaleranthis saniculifolia NC_012615 159924 NA 2010-03-26 2017-01-18
Mesostigma viride NC_002186 118360 NA 2009-04-15 2017-01-18
Micromonas sp. RCC299 NC_012575 72585 NA 2010-03-26 2017-01-19
Millettia pinnata NC_016708 152968 NA 2013-01-22 2017-01-19
Monomastix sp. OKE-1 NC_012101 114528 NA 2010-03-26 2017-01-18
Monomorphina aenigmatica NC_020018 74746 NA 2013-01-09 2017-01-19
Monsonia speciosa NC_014582 128787 NA 2011-01-06 2017-01-19
Morus indica NC_008359 158484 NA 2009-04-15 2017-01-18
Nandina domestica NC_008336 156599 NA 2009-04-15 2017-01-19
Nannochloropsis gaditana NC_020014 114989 NA 2012-12-31 2017-01-18
Nasturtium officinale NC_009275 155105 NA 2010-03-26 2017-01-18
Nelumbo lutea NC_015605 163206 NA 2011-06-01 2017-01-19
Nelumbo nucifera NC_015610 163307 NA 2011-06-01 2017-01-19
Neottia nidus-avis NC_016471 92060 NA 2011-12-21 2017-01-18
Nephroselmis olivacea NC_000927 200799 NA 2009-04-15 2017-01-19
Nicotiana sylvestris NC_007500 155941 NA 2010-03-26 2017-01-19
Nicotiana tabacum NC_001879 155943 NA 2009-04-15 2017-01-19
Nicotiana tomentosiformis NC_007602 155745 NA 2010-03-26 2017-01-19
Nicotiana undulata NC_016068 155863 NA 2012-02-27 2017-01-19
Nuphar advena NC_008788 160866 NA 2009-04-15 2017-01-19
Nymphaea alba NC_006050 159930 NA 2009-12-04 2017-01-19
Odontella sinensis NC_001713 119704 NA 2010-03-26 2017-01-19
Oedogonium cardiacum NC_011031 196547 NA 2010-03-26 2017-01-19
Oenothera argillicola NC_010358 165055 NA 2010-03-26 2017-01-18
Oenothera biennis NC_010361 164807 NA 2010-03-26 2017-01-19
Oenothera elata subsp. hookeri NC_002693 165728 NA 2010-03-26 2017-01-18
Oenothera glazioviana NC_010360 165225 NA 2010-03-26 2017-01-19
Oenothera parviflora NC_010362 163365 NA 2010-03-26 2017-01-18
Olea europaea NC_013707 155888 NA 2011-12-28 2017-01-18
Olea europaea subsp. cuspidata NC_015604 155862 NA 2011-08-01 2017-01-19
Olea europaea subsp. europaea NC_015401 155875 NA 2011-08-01 2017-01-19
Olea europaea subsp. maroccana NC_015623 155896 NA 2011-08-01 2017-01-18
Olea woodiana subsp. woodiana NC_015608 155942 NA 2011-08-01 2017-01-18
Olimarabidopsis pumila NC_009267 154737 NA 2010-03-26 2017-01-19
Oltmannsiellopsis viridis NC_008099 151933 NA 2010-05-03 2017-01-19
Oncidium hybrid cultivar NC_014056 146484 NA 2010-04-27 2017-01-19
Ophioglossum californicum NC_020147 138270 NA 2013-01-22 2017-01-19
Oryza meridionalis NC_016927 134558 NA 2012-02-28 2017-01-18
Oryza nivara NC_005973 134494 NA 2011-03-11 2017-01-18
Oryza rufipogon NC_017835 134544 NA 2012-05-09 2017-01-18
Oryza sativa Indica Group NC_008155 134496 NA 2009-04-15 2017-01-19
Oryza sativa Japonica Group NC_001320 134525 NA 2009-04-15 2017-01-19
Ostreococcus tauri NC_008289 71666 NA 2010-03-26 2017-01-18
Pachycladon cheesemanii NC_021102 154498 NA 2013-04-30 2017-01-18
Pachycladon enysii NC_018565 154896 NA 2012-09-14 2017-01-18
Panax ginseng NC_006290 156318 NA 2010-03-26 2017-01-19
Panicum virgatum NC_015990 139619 NA 2011-09-09 2017-01-19
Parachlorella kessleri NC_012978 123994 NA 2011-09-30 2017-01-18
Pavlova lutheri NC_020371 95281 NA 2013-02-28 2017-01-19
Pedinomonas minor NC_016733 98340 NA 2012-02-17 2017-01-19
Pelargonium x hortorum NC_008454 217942 NA 2010-03-26 2017-01-18
Pellia endiviifolia NC_019628 120546 NA 2013-01-22 2017-01-19
Pentactina rupicola NC_016921 156612 NA 2012-02-23 2017-01-19
Phaeocystis antarctica NC_016703 105512 NA 2013-07-14 2017-01-18
Phaeocystis globosa NC_021637 107461 NA 2013-07-03 2017-01-19
Phaeodactylum tricornutum NC_008588 117369 NA 2010-03-26 2017-01-19
Phalaenopsis aphrodite subsp. formosana NC_007499 148964 NA 2009-04-15 2017-01-19
Phalaenopsis equestris NC_017609 148959 NA 2012-08-09 2017-01-18
Pharus latifolius NC_021372 142077 NA 2013-06-10 2017-01-19
Phaseolus vulgaris NC_009259 150285 NA 2009-04-15 2017-01-19
Phoenix dactylifera NC_013991 158462 NA 2011-03-09 2017-01-19
Phyllostachys edulis NC_015817 139679 NA 2011-07-15 2017-01-18
Phyllostachys nigra var. henonis NC_015826 139839 NA 2011-07-15 2017-01-18
Phyllostachys propinqua NC_016699 139704 NA 2012-01-27 2017-01-19
Physcomitrella patens subsp. patens NC_005087 122890 NA 2010-03-26 2017-01-19
Picea abies NC_021456 124084 NA 2013-07-14 2017-01-19
Picea morrisonicola NC_016069 124168 NA 2012-08-09 2017-01-18
Picea sitchensis NC_011152 120176 NA 2010-03-26 2017-01-19
Pinus contorta NC_011153 120438 NA 2011-03-09 2017-01-19
Pinus gerardiana NC_011154 117618 NA 2011-03-09 2017-01-19
Pinus koraiensis NC_004677 117190 NA 2010-03-26 2017-01-18
Pinus krempfii NC_011155 116989 NA 2011-03-09 2017-01-19
Pinus lambertiana NC_011156 117239 NA 2011-03-09 2017-01-19
Pinus massoniana NC_021439 119739 NA 2013-06-17 2017-01-19
Pinus monophylla NC_011158 116479 NA 2011-03-09 2017-01-19
Pinus nelsonii NC_011159 116834 NA 2011-03-09 2017-01-18
Pinus taeda NC_021440 121530 NA 2013-06-17 2017-01-18
Pinus thunbergii NC_001631 119707 NA 1994-08-13 2017-01-19
Piper cenocladum NC_008457 160624 NA 2010-03-26 2017-01-18
Pisum sativum NC_014057 122169 NA 2010-12-07 2017-01-19
Platanus occidentalis NC_008335 161791 NA 2009-04-15 2017-01-19
Pleodorina starrii NC_021109 269857 NA 2013-04-30 2017-01-19
Podocarpus totara NC_020361 133259 NA 2013-02-28 2017-01-19
Populus alba NC_008235 156505 NA 2010-03-26 2017-01-19
Populus trichocarpa NC_009143 157033 NA 2010-03-26 2017-01-18
Porphyra purpurea NC_000925 191028 NA 2010-03-26 2017-01-18
Prinsepia utilis NC_021455 156328 NA 2013-07-15 2017-01-18
Prunus persica NC_014697 157790 NA 2011-01-06 2017-01-19
Pseudendoclonium akinetum NC_008114 195867 NA 2009-04-15 2017-01-19
Pseudophoenix vinifera NC_020364 157829 NA 2013-02-28 2017-01-19
Pseudotsuga sinensis var. wilsoniana NC_016064 122513 NA 2011-10-14 2017-01-18
Psilotum nudum NC_003386 138829 NA 2009-12-04 2017-01-18
Pteridium aquilinum subsp. aquilinum NC_014348 152362 NA 2010-07-27 2017-01-19
Ptilidium pulcherrimum NC_015402 119007 NA 2011-04-27 2017-01-19
Pycnococcus provasolii NC_012097 80211 NA 2010-03-26 2017-01-19
Pyramimonas parkeae NC_012099 101605 NA 2011-09-29 2017-01-18
Pyropia haitanensis NC_021189 195597 NA 2013-06-07 2017-01-19
Pyropia yezoensis NC_007932 191952 NA 2010-03-26 2017-01-18
Pyrus pyrifolia NC_015996 159922 NA 2011-09-14 2017-01-19
Quercus rubra NC_020152 161304 NA 2013-01-18 2017-01-19
Ranunculus macranthus NC_008796 155129 NA 2011-03-11 2017-01-18
Rhizanthella gardneri NC_014874 59190 NA 2011-06-17 2017-01-18
Rhodomonas salina NC_009573 135854 NA 2010-03-26 2017-01-19
Rhynchoryza subulata NC_016718 136303 NA 2012-01-27 2017-01-18
Ricinus communis NC_016736 163161 NA 2012-01-17 2017-01-18
Saccharina japonica NC_018523 130584 NA 2012-09-04 2017-01-18
Saccharum hybrid cultivar NCo 310 NC_006084 141182 NA 2011-09-09 2017-01-19
Saccharum hybrid cultivar SP80-3280 NC_005878 141182 NA 2011-02-14 2017-01-18
Salvia miltiorrhiza NC_020431 151328 NA 2013-03-04 2017-01-19
Schizomeris leibleinii NC_015645 182759 NA 2012-05-09 2017-01-19
Selaginella moellendorffii NC_013086 143780 NA 2010-11-03 2017-01-18
Sesamum indicum NC_016433 153324 NA 2012-02-28 2017-01-18
Silene conica NC_016729 147208 NA 2012-05-09 2017-01-19
Silene latifolia NC_016730 151736 NA 2012-05-09 2017-01-19
Silene noctiflora NC_016728 151639 NA 2012-05-09 2017-01-19
Solanum bulbocastanum NC_007943 155371 NA 2010-03-26 2017-01-19
Solanum lycopersicum NC_007898 155461 NA 2010-03-26 2017-01-18
Solanum tuberosum NC_008096 155296 NA 2010-04-15 2017-01-18
Sorghum bicolor NC_008602 140754 NA 2009-04-15 2017-01-19
Spinacia oleracea NC_002202 150725 NA 2009-04-15 2017-01-19
Spirodela polyrhiza NC_015891 168788 NA 2011-10-21 2017-01-18
Staurastrum punctulatum NC_008116 157089 NA 2009-04-15 2017-01-19
Stigeoclonium helveticum NC_008372 223902 NA 2010-03-26 2017-01-19
Syntrichia ruralis NC_012052 122630 NA 2012-03-16 2017-01-19
Taiwania cryptomerioides NC_016065 132588 NA 2012-09-14 2017-01-19
Taiwania flousiana NC_021441 131413 NA 2013-06-17 2017-01-19
Taxus mairei NC_020321 127665 NA 2013-02-25 2017-01-18
Tectona grandis NC_020098 153953 NA 2013-01-22 2017-01-18
Tetracentron sinense NC_021425 164467 NA 2013-06-10 2017-01-18
Thalassiosira oceanica CCMP1005 NC_014808 141790 NA 2011-03-02 2017-01-19
Thalassiosira pseudonana NC_008589 128814 NA 2010-03-26 2017-01-19
Theobroma cacao NC_014676 160619 NA 2011-08-01 2017-01-19
Trachelium caeruleum NC_010442 162321 NA 2009-04-15 2017-01-18
Trebouxiophyceae sp. MX-AZ01 NC_018569 149707 NA 2013-07-10 2017-01-19
Trifolium subterraneum NC_011828 144763 NA 2010-03-26 2017-01-19
Trithuria inconspicua NC_020372 165389 NA 2013-02-28 2017-01-18
Triticum aestivum NC_002762 134545 NA 2009-04-15 2017-01-18
Trochodendron aralioides NC_021426 165945 NA 2013-06-10 2017-01-19
Typha latifolia NC_013823 161572 NA 2010-07-02 2017-01-19
Utricularia gibba NC_021449 152113 NA 2013-07-02 2017-01-19
Vaccinium macrocarpon NC_019616 176045 NA 2012-12-20 2017-01-18
Vaucheria litorea NC_011600 115341 NA 2010-03-26 2017-01-18
Vigna angularis NC_021091 151683 NA 2013-05-17 2017-01-19
Vigna radiata NC_013843 151271 NA 2010-07-28 2017-01-18
Vigna unguiculata NC_018051 152415 NA 2012-07-02 2017-01-19
Vitis vinifera NC_007957 160928 NA 2010-05-03 2017-01-18
Welwitschia mirabilis NC_010654 119726 NA 2010-03-26 2017-01-19
Wolffia australiana NC_015899 168704 NA 2011-10-21 2017-01-19
Wolffiella lingulata NC_015894 169337 NA 2011-10-21 2017-01-19
Zea mays NC_001666 140384 NA 2009-04-15 2017-01-19
Zingiber spectabile NC_020363 155890 NA 2013-02-28 2017-01-18
Ziziphus jujuba NC_030299 161466 NA 2016-06-10 2017-01-15
Zoysia macrantha NC_029418 135845 NA 2016-03-01 2017-01-15
Zygnema circumcarinatum NC_008117 165372 NA 2009-04-15 2017-01-19


CpBase :: Chloroplast Genome Database

There are several ways you can look at the database:

Index of Genomes
This displays all chloroplast genomes publicly available from NCBI

Index of Gene Clusters
This a list of all Gene Clusters.

Index of RNA Clusters
This a list of all RNA Clusters.

About CpBase
CpBase technical info and credits.

 

Terence Leach

I am currently a freshman attending the University of Washington- Seattle, intending to major in Ecology, Evolution, and Conservation Biology with a minor in Marine Biology. I started working in the Rocap Lab with graduate student Michael Carlson over the summer while taking part in a program called GenOM ALVA, and have been conducting undergraduate research for the last two quarters. My current project is sequencing genes from Pseudo-nitzschia species and trying to reconstruct their evolutionary relationships. My long term interests include going to graduate school to further my studies in marine biology and to eventually become a marine biologist.

Clara Fuchsman

Research Interests:

I like to combine molecular and chemical techniques to answer biogeochemical questions.  In particular, I study the anaerobic nitrogen cycle. In this position, I have combined  metagenomics on samples from the Eastern Tropical North Pacific Oxygen Minimum Zone with in situ nitrogen gas measurements. Future work includes examining rates and proteins of nitrogen cycling microbes on sediment trap material in the OMZ.

Why Care About Oxygen Minimum Zones?

1. All organisms need a source of nitrogen. In anaerobic environments, usuable nitrogen is converted to N2 gas and lost from the ocean. The extent of Oxygen Minimum Zones should increase with warmer temperatures, potentially increasing N loss.

2. The greenhouse gas N2O accumulates under low but measurable oxygen.

3. Oxygen Minimum Zones and the Black Sea are modern analogs for the ancient Proterozoic Ocean, which lasted for over a billion years. 

4. Microbes in low oxygen environments are under studied and weird (and awesome!)

 

Education:

BA Biochemistry with High Honors, Swarthmore College (2001)

MS Chemical Oceanography, University of Washington (2004) Title: Microbial Activity Evidenced by N Species and Isotopes in the Black Sea Advisor: James Murray

PhD Chemical Oceanography, University of Washington (2010) Title: Microbial ecology and nitrogen isotope biogeochemistry of the Black Sea  Advisors: James Murray and James Staley

Certificate in Astrobiology, University of Washington (2010)  Astrobiology Rotation Title: Vertical Descent or Lateral Transfer? Unraveling the large number of shared genes between anaerobic and/or thermophilic bacteria and archaea Advisor: Gabrielle Rocap

Employment:

Research Scientist, University of Washington (2011-2012) with Allan Devol

Postdoctoral Scientist, University of Washington (2013-present) with Gabrielle Rocap

Mentoring:

I have mentored two undergraduates who came to the lab through the UW GenOM Project (ALVA) http://depts.washington.edu/genomics/hsprog/alva.shtml

I also participated in the summer Ocean Intern program for high school students: http://www.ocean.washington.edu/story/Ocean+Intern

I am currently mentoring two undergraduates through their senior thesis project for Oceanography: http://www.ocean.washington.edu/story/Oceanography_Senior_Thesis

Publications

Fuchsman, C.A., Devol, A.H., Rocap, G. (in review) Microbial ecological niche partitioning in the N cycling community of an offshore Oxygen Deficient Zone. ISME

Kirkpatrick, J.B.,* Fuchsman, C.A.,* Yakushev, E.V., Egorov, A.V., Staley, J.T., Murray, J.W. (in review) Dark Nitrogen Fixation in the Redoxcline of the Black Sea. PLOS One.

Fuchsman, C.A., Paul, B., Yakushev, E., and Murray, J.W. (in revision) Detection of transient denitrification during a high organic matter event in the Black Sea. Global Biogeochemical Cycles

Peng, X., Fuchsman, C.A., Jayakumar A., Warner, M.J., Devol, A.H., Ward, B.B. (2016) Revisiting Nitrification in the Eastern Tropical South Pacific: A focus on its controls. Journal of Geophysical Research—Oceans 121: doi:10.1002/ 2015JC011455.  

Peng, X.  C. A. Fuchsman, W. Martens-Habbena, A. H. Devol, A. Jayakumar, B. B. Ward. (2015) Ammonium and nitrite oxidation in the Eastern Tropical North Pacific. GBC: doi:10.1002/2015GB005278 

Fuchsman, C.A., A.H. Devol, Z. Chase, C.E. Reimers, B. Hales (2015) Benthic fluxes on the Oregon shelf. Estuarine, Coastal and Shelf Science 163: 156-166. PDF

Kirkpatrick J.B., Fuchsman, C.A., Yakushev, E.V., Staley, J.T., and Murray, J.W. (2012) Activity of Anammox and Denitrifying Bacteria in the Black Sea. Frontiers in Aquatic Microbiology 3: 255. PDF

Fuchsman, C.A., Murray, J.W., and Staley, J.T. (2012) Stimulation of autotrophic denitrification by intrusions of the Bosporus Plume into the anoxic Black Sea. Frontiers in Aquatic Microbiology 3: 257

Fuchsman, C.A., Staley, J.T., Oakley, B.O., Kirkpatrick J.B. and Murray, J.W. (2012) Free-living and aggregate associated Planctomycetes in the Black Sea. FEMS Microbiology Ecology 80: 402-416. PDF

Fuchsman, C.A., Kirkpatrick, J.B., Brazelton, W.J., Murray, J.W., and Staley, J.T. (2011) Metabolic strategies of free-living and aggregate associated bacterial communities inferred from biological and chemical profiles in the Black Sea suboxic zone. FEMS Microbiology Ecology 78: 586-603. PDF

Fuchsman, C.A., Murray, J.W., and Konovalov, S.K. (2008) Concentration and natural stable isotope profiles of nitrogen species in the Black Sea. Marine Chemistry 111: 90-105.

Konovalov, S.K., Fuchsman, C.A., Belokopitov, V., Murray, J.W. (2008) Modeling the distribution of nitrogen species and isotopes in the water column of the Black Sea. Marine Chemistry 111: 106-124. 

Oakley, B.B., Francis, C.A., Roberts, K.J., Fuchsman, C.A., Srinivasan, S., and Staley, J.T. (2007) Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria in the Black Sea suboxic zone. Environmental Microbiology 9: 118-130.

Fuchsman, C.A., and Rocap, G. (2006) Whole-genome reciprocal BLAST analysis reveals that Planctomycetes do not share an unusually large number of genes with Eukarya and Archaea. Applied and Environmental Microbiology 72: 6841-6844. PDF

Kirkpatrick J., Oakley, B., Fuchsman, C., Srinivasan, S., Staley, J.T., and Murray, J.W. (2006) Diversity and distribution of Planctomycetes and related bacteria in the suboxic zone of the Black Sea. Applied and Environmental Microbiology 72: 3079-3083. 

Personal Interests:

Soccer: I manage and play on the FC Flowbees, a co-ed outdoor soccer team. 

Nature Photography:


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