Fraktale Datenanalyse

Fraktale Dimension ist ein Maß, das die Komplexität von Datenmengen erfassen kann. In diesem Projekt sollen Methoden zum Bestimmen einer fraktalen Dimension zur Analyse von Datenmengen genutzt werden. Bisherige Anwendung ist die Analyse von Transit-Peptiden.

Teilprojekte

  • Dimension Induced Clustering
  • Vergleich der fraktalen Dimension von pflanzlichen und nicht-pflanzlichen mitochondriellen Transit-Peptiden
  • Bootstrap-Test, ob zwei Datenmengen verschiedene fraktale Dimension haben
  • Bootstrap-Test zum Bestimmen der Anzahl der dimensions-induzierten Cluster
  • Bestimmen von spezifischen Aminosäure-Substitutions-Matrizen für Transit-Peptide

Forschungsseminar Fraktale Dimension

  • Prof. Ludwig Staiger, Dr. Alexander Hinneburg, Marian Kogeler
  • Do. 14-16 Uhr, Raum 2.11
  • Beginn am 29.4.2010
  • Nächstes Treffen: Do. 20.5.2010

Technische Hinweise

Die bisher entwickelten Algorithmen sind in Matlab geschrieben, dass in den Pools installiert ist. Um größere Rechungen durchzuführen, sollte octave (ein freier Matlab-Clone) auf verdi.informatik.uni-halle.de genutzt werden. Damit octave-3.2.4 genutzt wird müssen Umgebungsvariablen mit den folgenden Befehlen gesetzt werden:

export LD_LIBRARY_PATH=/oai/product/10.2.0/Db_1/lib:\
          /opt/csw/gcc4/lib:/opt/csw/lib::/usr/local/lib
export PATH=/opt/octave/bin:$PATH

Dann kann octave gestartet werden. Bisher installierte Pakete von octave-forge:

  • miscellaneous-1.0.9
  • optim-1.0.12

Eine aktuelle Liste der Pakete zeigt der Befehl

octave:1> pkg list
Package Name   | Version | Installation directory
---------------+---------+-----------------------
miscellaneous *|   1.0.9 | /opt/octave/share/octave/packages/miscellaneous-1.0.9
        optim *|  1.0.12 | /opt/octave/share/octave/packages/optim-1.0.12

Studentische Arbeiten

Peter Höhne

Thema: Bootstrap test for different fractal dimensionality

→ Weiter lesen...

Ulrike Felgenhauer

Dimension Induced Clustering on Transit Peptides

Teil des Projektes Fraktale Datenanalyse

Daniel Vinzenz

Thema: Context Specific Substitution Matrices for Transit Peptides

Teil des Projektes Fraktale Datenanalyse

Jennifer Conrad

Datei mit Auflistung der vorhanden Organismen

 Anzahl Organism
      1 Acanthamoeba castellanii (Amoeba)
      9 Aedes aegypti (Yellowfever mosquito) (Culex aegypti)
      3 Agaricus bisporus (Common mushroom)
      1 Agrocybe aegerita (Black poplar mushroom)
      1 Ailuropoda melanoleuca (Giant panda)
      3 Ajellomyces capsulata (Darling's disease fungus) (Histoplasma capsulatum)
      1 Ajellomyces capsulata (strain ATCC 26029 / G186AR / H82 / RMSCC 2432) (Darling's disease fungus) (Histoplasma capsulatum)
      5 Ajellomyces capsulata (strain NAm1 / WU24) (Darling's disease fungus) (Histoplasma capsulatum)
      1 Ajellomyces dermatitidis (strain ER-3) (Blastomyces dermatitidis)
      1 Ajellomyces dermatitidis (strain SLH14081) (Blastomyces dermatitidis)
      1 Alnus glutinosa (Alder)
      1 Alternaria alternata (Alternaria rot fungus)
      1 Amaranthus hypochondriacus (Prince-of-Wales feather)
      1 Amblyrhynchus cristatus (Marine iguana)
      6 Anopheles gambiae (African malaria mosquito)
      1 Anser anser anser (Western graylag goose)
      1 Aotus azarai (Southern owl monkey) (Aotus azarae)
    337 Arabidopsis thaliana (Mouse-ear cress)
      1 Artemia sanfranciscana (Brine shrimp) (Artemia franciscana)
      1 Arxula adeninivorans (Yeast)
      6 Ascaris suum (Pig roundworm) (Ascaris lumbricoides)
     56 Ashbya gossypii (Yeast) (Eremothecium gossypii)
     11 Aspergillus clavatus
      5 Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167)
     23 Aspergillus fumigatus (Sartorya fumigata)
      5 Aspergillus fumigatus (strain CEA10 / CBS 144.89 / FGSC A1163) (Sartorya fumigata)
      7 Aspergillus niger
     12 Aspergillus niger (strain CBS 513.88 / FGSC A1513)
     17 Aspergillus oryzae
      1 Aspergillus terreus
     12 Aspergillus terreus (strain NIH 2624 / FGSC A1156)
      2 Ateles belzebuth (Long-haired spider monkey)
      2 Blastocladiella emersonii (Aquatic fungus)
      1 Blumeria graminis
      1 Bombyx mori (Silk moth)
    302 Bos taurus (Bovine)
      1 Botryotinia fuckeliana (Noble rot fungus) (Botrytis cinerea)
      5 Botryotinia fuckeliana (strain B05.10) (Noble rot fungus) (Botrytis cinerea)
      2 Brassica napus (Rape)
      2 Brassica oleracea (Wild cabbage)
     23 Caenorhabditis briggsae
     89 Caenorhabditis elegans
      1 Callicebus donacophilus (Bolivian titi)
      1 Callicebus moloch (Dusky titi monkey)
      5 Callithrix jacchus (Common marmoset)
      1 Candida albicans (strain WO-1) (Yeast)
     44 Candida albicans (Yeast)
      5 Candida dubliniensis (strain CD36 / CBS 7987 / NCPF 3949 / NRRL Y-17841) (Yeast)
     52 Candida glabrata (Yeast) (Torulopsis glabrata)
      2 Candida maltosa (Yeast)
      1 Candida parapsilosis (Yeast)
      1 Candida tropicalis (strain ATCC MYA-3404 / T1) (Yeast)
      5 Candida tropicalis (Yeast)
      2 Canis familiaris (Dog) (Canis lupus familiaris)
      1 Capra hircus (Goat)
      1 Capsicum annuum (Bell pepper)
      2 Cavia porcellus (Guinea pig)
      1 Cebuella pygmaea (Pygmy marmoset) (Callithrix pygmaea)
      1 Cebus apella (Brown-capped capuchin)
      3 Cercopithecus aethiops (Green monkey) (Grivet)
     10 Chaetomium globosum (Soil fungus)
      1 Charybdis feriatus (Crucifix crab) (Cancer feriatus)
      6 Chlamydomonas reinhardtii
      1 Choristoneura fumiferana (Spruce budworm)
      1 Citrullus lanatus (Watermelon) (Citrullus vulgaris)
      1 Citrus maxima (Pomelo) (Citrus grandis)
      1 Clavispora lusitaniae (strain ATCC 42720) (Yeast) (Candida lusitaniae)
     12 Coccidioides immitis (Valley fever fungus)
      1 Coccidioides posadasii (strain C735) (Valley fever fungus)
      1 Colobus guereza (Black-and-white colobus monkey)
      1 Colobus polykomos (Western black-and-white colobus monkey)
      1 Columba livia (Domestic pigeon)
      1 Coprinellus disseminatus (Fairy ink cap fungus)
      4 Coprinopsis cinerea (strain Okayama-7 / 130 / FGSC 9003) (Inky cap fungus) (Hormographiella aspergillata)
      1 Coprinopsis scobicola (Ink cap fungus)
      7 Cricetulus griseus (Chinese hamster)
      1 Cricetus cricetus (Black-bellied hamster)
      1 Cryptococcus gattii (Filobasidiella gattii) (Cryptococcus bacillisporus)
     22 Cryptococcus neoformans (Filobasidiella neoformans)
      4 Cryptococcus neoformans var. grubii (Filobasidiella neoformans var. grubii)
      1 Cryptosporidium hominis
      1 Cryptosporidium parvum
      2 Cucurbita maxima (Pumpkin) (Winter squash)
      5 Culex quinquefasciatus (Southern house mosquito) (Culex pungens)
      1 Cyanophora paradoxa
      2 Cyprinus carpio (Common carp)
     73 Danio rerio (Zebrafish) (Brachydanio rerio)
      1 Dasyatis americana (Southern stingray)
      2 Daucus carota (Carrot)
     41 Debaryomyces hansenii (Yeast) (Torulaspora hansenii)
      2 Delphinapterus leucas (Beluga whale)
    132 Dictyostelium discoideum (Slime mold)
      1 Drosophila acanthoptera (Fruit fly)
      8 Drosophila ananassae (Fruit fly)
      7 Drosophila erecta (Fruit fly)
      6 Drosophila grimshawi (Fruit fly) (Idiomyia grimshawi)
    114 Drosophila melanogaster (Fruit fly)
      1 Drosophila mettleri (Fruit fly)
      5 Drosophila mojavensis (Fruit fly)
      6 Drosophila persimilis (Fruit fly)
     19 Drosophila pseudoobscura pseudoobscura (Fruit fly)
      7 Drosophila sechellia (Fruit fly)
      6 Drosophila simulans (Fruit fly)
      8 Drosophila virilis (Fruit fly)
      7 Drosophila willistoni (Fruit fly)
      7 Drosophila yakuba (Fruit fly)
     30 Emericella nidulans (Aspergillus nidulans)
      3 Equus caballus (Horse)
      1 Eucalyptus gunnii (Cider tree)
      6 Euglena gracilis
      4 Eulemur fulvus fulvus (Brown lemur)
      1 Felis catus (Cat) (Felis silvestris catus)
      3 Flaveria anomala (Yellowtops)
      1 Flaveria australasica (Australian yellow weed)
      6 Flaveria pringlei
      1 Flaveria pubescens (Yellowtops)
      3 Flaveria trinervia (Clustered yellowtops) (Oedera trinervia)
      2 Fragaria ananassa (Strawberry)
      1 Fusarium oxysporum (Panama disease fungus)
      1 Fusarium solani subsp. phaseoli (Nectria haematococca)
      2 Galago crassicaudatus (Thick-tailed galago) (Otolemur crassicaudatus)
     46 Gallus gallus (Chicken)
      1 Ganoderma microsporum
      2 Gecko japonicus (Japanese gecko)
      1 Gelasinospora sp. (strain S23)
     14 Gibberella zeae (Wheat head blight fungus) (Fusarium graminearum)
      2 Glossina morsitans morsitans (Savannah tsetse fly)
      7 Glycine max (Soybean) (Glycine hispida)
     25 Gorilla gorilla gorilla (Lowland gorilla)
      1 Gossypium hirsutum (Upland cotton) (Gossypium mexicanum)
      1 Gracilaria verrucosa (Red alga)
      2 Hansenula anomala (Yeast) (Candida pelliculosa)
      1 Hartmannella vermiformis (Amoeba)
      1 Heliothis virescens (Tobacco budworm moth)
      1 Hemicentrotus pulcherrimus (Sea urchin)
      2 Hevea brasiliensis (Para rubber tree)
    479 Homo sapiens (Human)
      1 Hordeum vulgare (Barley)
      1 Hylobates agilis (Agile gibbon)
      3 Hylobates lar (Common gibbon)
      2 Hylobates syndactylus (Siamang) (Symphalangus syndactylus)
      1 Iguana iguana (Common iguana)
      3 Ipomoea batatas (Sweet potato) (Convolvulus batatas)
      1 Katsuwonus pelamis (Skipjack tuna) (Bonito)
     64 Kluyveromyces lactis (Yeast) (Candida sphaerica)
      2 Kluyveromyces marxianus (Yeast) (Candida kefyr)
      4 Laccaria bicolor (strain S238N-H82) (Bicoloured deceiver) (Laccaria laccata var. bicolor)
      1 Lachancea thermotolerans (strain CBS 6340) (Yeast) (Kluyveromyces thermotolerans)
      1 Lagothrix lagotricha (Common woolly monkey)
      2 Leishmania braziliensis
      2 Leishmania infantum
      4 Leishmania major
      3 Leishmania tarentolae (Sauroleishmania tarentolae)
      1 Lentinula edodes (Shiitake mushroom) (Lentinus edodes)
      1 Leucoagaricus gongylophorus (Leaf-cutting ant fungus)
     13 Lodderomyces elongisporus (Yeast) (Saccharomyces elongisporus)
      1 Lupinus angustifolius (Narrow-leaved blue lupin)
     57 Macaca fascicularis (Crab eating macaque) (Cynomolgus monkey)
      1 Macaca fuscata fuscata (Japanese macaque)
      3 Macaca mulatta (Rhesus macaque)
      1 Macaca nemestrina (Pig-tailed macaque)
      2 Macaca silenus (Lion-tailed macaque)
      1 Macropus parma (Parma wallaby)
     11 Magnaporthe grisea (Rice blast fungus) (Pyricularia grisea)
      2 Malassezia globosa (strain ATCC 96807 / CBS 7966) (Dandruff-associated fungus)
      2 Manduca sexta (Tobacco hawkmoth) (Tobacco hornworm)
      1 Mangifera indica (Mango)
      2 Mesembryanthemum crystallinum (Common ice plant) (Cryophytum crystallinum)
      6 Mesocricetus auratus (Golden hamster)
      1 Monilinia fructicola
      1 Mus caroli (Wild mouse) (Ricefield mouse)
    454 Mus musculus (Mouse)
      1 Mus saxicola (Spiny mouse)
      1 Mycosphaerella graminicola (Septoria tritici)
      1 Nannizzia otae (strain CBS 113480) (Microsporum canis) (Arthroderma otae)
      4 Nematostella vectensis (Starlet sea anemone)
     11 Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) (Aspergillus fischerianus)
     77 Neurospora crassa
      2 Nicotiana benthamiana
      2 Nicotiana plumbaginifolia (Leadwort-leaved tobacco)
      2 Nicotiana sylvestris (Wood tobacco)
     10 Nicotiana tabacum (Common tobacco)
      1 Nomascus gabriellae (Red-cheeked gibbon)
      2 Nycticebus coucang (Slow loris)
      1 Oenothera elata subsp. hookeri (Hooker's evening primrose) (Oenothera hookeri)
      1 Onchocerca volvulus
      1 Oncorhynchus masou (Cherry salmon) (Masu salmon)
      3 Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri)
      2 Opsanus tau (Oyster toadfish)
     13 Oryctolagus cuniculus (Rabbit)
      5 Oryza sativa subsp. indica (Rice)
     39 Oryza sativa subsp. japonica (Rice)
      1 Osmerus mordax (Rainbow smelt) (Atherina mordax)
      1 Ostreococcus tauri
      6 Ovis aries (Sheep)
      1 Pachysolen tannophilus (Yeast)
      5 Pan paniscus (Pygmy chimpanzee) (Bonobo)
     33 Pan troglodytes (Chimpanzee)
      3 Papio anubis (Olive baboon)
      3 Papio hamadryas (Hamadryas baboon)
      1 Papio hamadryas ursinus (Chacma baboon)
      3 Paracoccidioides brasiliensis
      2 Paracoccidioides brasiliensis (strain ATCC MYA-826 / Pb01)
      1 Paracoccidioides brasiliensis (strain Pb03)
      1 Paracoccidioides brasiliensis (strain Pb18)
      2 Paramecium tetraurelia
      1 Penicillium chrysogenum (Penicillium notatum)
      5 Penicillium chrysogenum (strain ATCC 28089 / DSM 1075 / Wisconsin 54-1255) (Penicillium notatum)
      4 Penicillium marneffei (strain ATCC 18224 / CBS 334.59 / QM 7333)
     10 Phaeosphaeria nodorum (Glume blotch fungus) (Septoria nodorum)
      1 Phaseolus vulgaris (Kidney bean) (French bean)
      1 Phytophthora infestans (Potato late blight fungus)
     15 Pichia guilliermondii (Yeast) (Candida guilliermondii)
      2 Pichia pastoris (strain GS115) (Yeast)
      1 Pichia pastoris (Yeast)
     17 Pichia stipitis (Yeast)
     12 Pisum sativum (Garden pea)
      1 Plasmodium chabaudi
      3 Plasmodium falciparum (isolate 3D7)
      1 Plasmodium falciparum (isolate FCR-3 / Gambia)
      1 Plasmodium knowlesi (strain H)
      1 Plasmodium vivax
      1 Plasmodium yoelii yoelii
      1 Pleurotus djamor (Pink oyster mushroom)
      5 Podospora anserina
    121 Pongo abelii (Sumatran orangutan)
     27 Pongo pygmaeus (Bornean orangutan)
      2 Presbytis cristata (Silvered langur)
      1 Prunus persica (Peach)
      3 Pyrenophora tritici-repentis (strain Pt-1C-BFP) (Wheat tan spot fungus) (Drechslera tritici-repentis)
      4 Rana catesbeiana (Bull frog)
    268 Rattus norvegicus (Rat)
      1 Reclinomonas americana
      2 Rhinolophus ferrumequinum (Greater horseshoe bat)
      1 Rhizopus oryzae (Rhizopus delemar)
      1 Saccharomyces bayanus (Yeast) (Saccharomyces uvarum)
    328 Saccharomyces cerevisiae (Baker's yeast)
      6 Saccharomyces cerevisiae (strain AWRI1631) (Baker's yeast)
      2 Saccharomyces cerevisiae (strain JAY291) (Baker's yeast)
      3 Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse) (Baker's yeast)
      9 Saccharomyces cerevisiae (strain RM11-1a) (Baker's yeast)
     19 Saccharomyces cerevisiae (strain YJM789) (Baker's yeast)
      2 Saccharomyces douglasii (Yeast)
      3 Saccharomyces kluyveri (Yeast) (Saccharomyces silvestris)
      1 Saccharomyces servazzii (Yeast)
      1 Saguinus labiatus (Red-chested mustached tamarin)
      5 Saimiri sciureus (Common squirrel monkey)
      1 Salmo salar (Atlantic salmon)
      1 Salvelinus alpinus (Arctic char)
      2 Salvelinus fontinalis (Brook trout) (Brook char)
      1 Schizophyllum commune (Bracket fungus)
      4 Schizosaccharomyces japonicus (strain yFS275 / FY16936) (Fission yeast)
    230 Schizosaccharomyces pombe (Fission yeast)
      7 Sclerotinia sclerotiorum (strain ATCC 18683 / 1980 / Ss-1) (White mold) (Whetzelinia sclerotiorum)
      1 Sminthopsis macroura (Stripe-faced dunnart)
      1 Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
     20 Solanum tuberosum (Potato)
      1 Sorex araneus (Eurasian common shrew) (European shrew)
      1 Spermophilus tridecemlineatus (Thirteen-lined ground squirrel)
      3 Spinacia oleracea (Spinach)
      1 Squalus acanthias (Spiny dogfish)
     51 Sus scrofa (Pig)
      2 Takifugu rubripes (Japanese pufferfish) (Fugu rubripes)
      4 Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006) (Penicillium stipitatum)
      3 Tarsius syrichta (Philippine tarsier)
      1 Tetrahymena thermophila
      1 Tetraodon nigroviridis (Green puffer)
      1 Tetrapturus audax (Striped marlin)
      2 Theropithecus gelada (Gelada baboon)
      1 Thunnus albacares (Yellowfin tuna) (Neothunnus macropterus)
      3 Thunnus obesus (Bigeye tuna)
      1 Trachypithecus cristatus (Silvered leaf monkey)
      1 Trametes hirsuta (White-rot fungus) (Coriolus hirsutus)
      2 Triticum aestivum (Wheat)
      6 Trypanosoma brucei brucei
      4 Trypanosoma cruzi
      1 Typhonium venosum (Voodoo lily) (Sauromatum guttatum)
      1 Uncinocarpus reesii (strain UAMH 1704)
      2 Uromyces fabae (Rust fungus)
     13 Ustilago maydis (Smut fungus)
     11 Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294) (Kluyveromyces polysporus)
      1 Venturia inaequalis (Apple scab fungus)
      2 Vigna unguiculata (Cowpea)
     60 Xenopus laevis (African clawed frog)
     37 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
      1 Xiphias gladius (Swordfish)
     37 Yarrowia lipolytica (Candida lipolytica)
     12 Zea mays (Maize)
      1 Zygosaccharomyces rouxii (strain ATCC 2623 / CBS 732 / IFO 1130 / NBRC 1623 / NCYC 568) (Candida mogii)

→ Weiter lesen...

 
de/research/project/fractal_data_analysis/fractal_data_analysis.txt · Zuletzt geändert: 2010/07/15 10:09 von hinnebur     Nach oben