Morad_Mokhtar

About SSRome

          Microsatellites, also referred to as simple sequence repeats (SSRs) or short tandem repeats (STRs) - are co-dominant molecular markers universally scattered within all organisms genomes. Microsatellites markers are highly popular due to their abundance, hyper-variability, multi-allelic, highly reproducibility and detection simplicity. Over past decades, they are extensively used in a variety of fundamental and applied biological sciences for prokaryotes, plants and animals studies. Microsatellites are also have extensively been exploited as genetic markers for diverse applications including genome mapping, genetic material characterization, population genetics and genome evolution studies.

     Nowadays, with the development of genome sequencing technologies, hundreds of genome sequences have been decoded and released. This published genomes data and the availability of bioinformatics tools provides an important opportunity for scientists to identify simple sequence repeats that could be used to develop useful SSR markers. These markers can be used subsequently in different studies such as; variety identification, genetic diversity evaluation, construction of genetic linkage maps, association mapping, and marker-assisted selection.

          SSRome is a comprehensive, integrated database and pipelines for microsatellites mining, classification, comparative analysis and markers development across all organisms.

SSRome Database

         SSRome is a user-friendly, integrated, comprehensive and dynamic database and pipelines for exploring microsatellites in a wide range of organisms. In SSRome database, 40,296,920 microsatellite DNA motifs were identified across Plants, Metazoa, Prokaryotes, Mitochondrial and Chloroplast sequenced genomes, in addition to all available NCBI ESTs till March 2017, represent collectively 5492 living organisms. This huge number of identified SSRs motifs were detected based on analysis of 76,621,110,515 bases of DNA. Moreover, a total of 13,987,159.00 SSR primer pairs were designed, using Primer3 software. All stored datasets of microsatellites motifs and markers of 5492 living organisms can be downloaded freely in very convenient way. SSRome database will be updated constantly. In SSRome database, 3 main functional modules\pages were developed to cover all content of identified SSR motifs among analyzed 5492 living organisms including 'Database Search', 'Downloads' and 'Statistics'.

         In addition to the SSRome database, SSRome provides three user-friendly pipelines, can help scientists\users to identify, classify and compare microsatellite motifs in both genomic and transcriptomic Genome-wide levels. This SSRome pipeline part also comes into 3 main functional modules\pages were developed to cover different types of SSRs mining analysis at Genome-wide level; including SSRome Genomic Pipeline', ' SSRome Transcriptomic Pipeline' and ' SSRome Comparative Analysis Pipeline'.

SSRome Genomic Pipeline (SGP)

          SSRome Genomic Pipeline (SGP) is a user-friendly tool can help scientists to identify and localize microsatellites at the Genome-wide level. The SGP tool can classify generated results into ‘SSR repeats unique to genic regions’, ‘SSR repeats unique to intergenic regions’ and ‘SSR repeats overlapped between genic and intergenic regions’. In addition, SSRome Genomic Pipeline includes adjustable SSR repeat unit and primer design parameters and user selectivity to design SSR primers in genic regions only, or in intergenic regions only or in both across the whole genomic regions.

SSRome Transcriptomic Pipeline (STP)

          SSRome Transcriptomic Pipeline (STP) is a user-friendly tool can identify and localize microsatellites at whole Transcriptomic-wide level (RNA-Seq data) or short cDNA sequences. The STP pipeline can perform SSRs mining at both assembled RNA Sequences with or without annotation information. In the case of providing STP with RNA Sequences without annotation information, STP will BLAST the RNA-sequences against local NCBI database to elucidate their best matching. In addition, SSRome Transcriptomic Pipeline includes adjustable SSR repeat unit and primer design parameters.

SSRome Comparative Analysis Pipeline (SCAP)

          SSRome Comparative Analysis Pipeline (SCAP) is a user-friendly pipeline can compare identified SSR motifs of any organism as generated using SSRome pipelines or any other SSR detection tools against the SSRome database. The SCAP pipeline will deliver comparing results in form of unique SSR motifs of submitted sequence (if found) and full comparative profile of this sequence in relevant of other organisms available in SSRome database.

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Amphimedon queenslandica

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Acanthaster planci

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Acropora digitifera

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Acyrthosiphon pisum

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Amphimedon queenslandica

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Anas platyrhynchos

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Anolis carolinensis

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Anopheles gambiae

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Apis mellifera

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Apteryx australis mantelli

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Astyanax mexicanus

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Atta cephalotes

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Balaenoptera acutorostrata scammoni

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Boleophthalmus pectinirostris

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Bombus impatiens

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Bombyx mori

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Bos mutus

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Bos taurus

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Branchiostoma floridae

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Brugia malayi

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Bubalus bubalis

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Caenorhabditis briggsae

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Camelus dromedarius

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Camelus ferus

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Camponotus floridanus

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Canis lupus familiaris

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Capra hircus

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Castor canadensis

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Chelonia mydas

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Chlorocebus sabaeus

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Chrysemys picta

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Ciona intestinalis

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Columba livia

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Corvus cornix

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Coturnix japonica

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Crassostrea gigas

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Cricetulus griseus

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Culex quinquefasciatus

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Cynoglossus semilaevis

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Danio rerio

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Diuraphis noxia

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Drosophila melanogaster

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Egretta garzetta

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Equus asinus

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Equus caballus

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Equus przewalskii

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Esox lucius

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Exaiptasia pallida

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Falco cherrug

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Felis catus

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Ficedula albicollis

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Folsomia candida

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Gallus gallus

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Geospiza fortis

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Gorilla gorilla gorilla

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Harpegnathos saltator

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Helobdella robusta

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Heterocephalus glaber

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Hippocampus comes

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Hipposideros armiger

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Homo sapiens

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Hydra vulgaris

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Ictalurus punctatus

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Larimichthys crocea

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Latimeria chalumnae

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Linepithema humile

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Lingula anatina

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Lipotes vexillifer

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Loa loa

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Lottia gigantea

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Loxodonta africana

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Macaca fascicularis

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Macaca mulatta

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Maylandia zebra

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Meleagris gallopavo

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Mizuhopecten yessoensis

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Musca domestica

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Mus musculus

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Myotis brandtii

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Myotis davidii

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Nannospalax galili

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Nanorana parkeri

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Nasonia vitripennis

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Necator americanus

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Nematostella vectensis

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Nicrophorus vespilloides

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Nomascus leucogenys

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Nothobranchius furzeri

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Notothenia coriiceps

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Octopus bimaculoides

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Odobenus rosmarus divergens

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Opisthorchis viverrini

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Orcinus orca

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Ornithorhynchus anatinus

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Oryctolagus cuniculus

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Oryzias latipes

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Ovis aries

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Panthera tigris altaica

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Pantholops hodgsonii

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Pan paniscus

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Pan troglodytes

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Papilio machaon

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Parus major

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Pediculus humanus corporis

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Pelodiscus sinensis

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Pieris rapae

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Plutella xylostella

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Poecilia reticulata

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Pogona vitticeps

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Pogonomyrmex barbatus

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Pongo abelii

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Pseudopodoces humilis

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Pteropus alecto

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Python bivittatus

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Rattus norvegicus

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Rhinolophus sinicus

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Rhinopithecus roxellana

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Saccoglossus kowalevskii

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Saimiri boliviensis boliviensis

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Schistosoma haematobium

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Schistosoma mansoni

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Scleropages formosus

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Sinocyclocheilus anshuiensis

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Sinocyclocheilus grahami

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Sinocyclocheilus rhinocerous

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Solenopsis invicta

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Strongylocentrotus purpuratus

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Struthio camelus australis

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Taeniopygia guttata

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Takifugu rubripes

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Tetranychus urticae

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Tribolium castaneum

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Trichinella spiralis

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Trichogramma pretiosum

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Xenopus tropicalis

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Xiphophorus maculatus

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Zootermopsis nevadensis

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Aegilops tauschii

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Amborella trichopoda

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Ananas comosus

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Arabidopsis lyrata

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Arabidopsis thaliana

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Arachis duranensis

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Arachis ipaensis

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Asparagus officinalis

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Auxenochlorella protothecoides

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Bathycoccus prasinos

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Beta vulgaris

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Brachypodium distachyon

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Brassica napus

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Brassica oleracea

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Brassica rapa

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Cajanus cajan

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Camelina sativa

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Capsella rubella

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Capsicum annuum

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Carica papaya

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Chenopodium quinoa

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Chlamydomonas reinhardtii

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Chlorella variabilis

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Chondrus crispus

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Cicer arietinum

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Citrus clementina

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Citrus sinensis

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Coccomyxa subellipsoidae

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Cucumis melo

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Cucumis sativus

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Cucurbita maxima

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Cucurbita moschata

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Cucurbita pepo

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Cyanidioschyzon merolae

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Daucus carota

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Dendrobium catenatum

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Durio zibethinus

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Elaeis guineensis

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Erythranthe guttata

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Eucalyptus grandis

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Eutrema salsugineum

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Fragaria vesca

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Galdieria sulphuraria

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Glycine max

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Gossypium hirsutum

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Gossypium raimondii

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Herrania umbratica

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Hevea brasiliensis

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Ipomoea nil

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Jatropha curcas

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Juglans regia

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Lactuca sativa

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Lupinus angustifolius

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Malus domestica

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Manihot esculenta

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Medicago truncatula

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Micromonas pusilla

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Momordica charantia

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Monoraphidium neglectum

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Morus notabilis

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Musa acuminata

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Nelumbo nucifera

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Nicotiana sylvestris

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Nicotiana tomentosiformis

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Olea europaea

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Oryza brachyantha

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Oryza sativa Japonica

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Ostreococcus lucimarinus

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Ostreococcus tauri

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Phalaenopsis equestris

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Phaseolus vulgaris

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Physcomitrella patens

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Populus euphratica

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Populus trichocarpa

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Prunus avium

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Prunus mume

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Prunus persica

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Pyrus x bretschneideri

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Quercus suber

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Raphanus sativus

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Ricinus communis

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Rosa chinensis

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Selaginella moellendorffii

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Sesamum indicum

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Setaria italica

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Solanum lycopersicum

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Solanum pennellii

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Solanum tuberosum

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Sorghum bicolor

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Spinacia oleracea

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Tarenaya hassleriana

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Theobroma cacao

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Vigna angularis

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Vigna radiata

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Vitis vinifera

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Volvox carteri

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Zea mays

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Ziziphus jujuba

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Archaea

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Archaea Annotated Genomes available in NCBI till May 2018

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Bacteria

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Bacteria Annotated Genomes available in NCBI till May 2018

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Virus

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Virus Annotated Genomes available in NCBI till May 2018

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Fungi

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Fungi Annotated Genomes available in NCBI till May 2018

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Protozoa

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Protozoa Annotated Genomes available in NCBI till May 2018

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Plant ESTs


Plants ESTs available in NCBI ESTdb till May 2018

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Metazoa ESTs


Animals ESTs available in NCBI ESTdb till May 2018

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Others ESTs


Others ESTs available in NCBI ESTdb till May 2018

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Plant Mitochondria


Plants mitochondria available in NCBI organelle genome resources till May 2018

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Metazoa Mitochondria


Animals mitochondria available in NCBI organelle genome resources till May 2018

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Plant Chloroplast


Plants chloroplast available in NCBI organelle genome resources till May 2018

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How to cite:

Morad M. Mokhtar and Mohamed A.M.Atia.   SSRome: An integrated database and pipelines for exploring microsatellites in all organisms.   link

Contact:

Principal Investigator: Ass. Prof. Mohamed A.M. Atia. matia@ageri.sci.eg   link

Pipelines programmer, Data analysis, Database and web developer: Morad M. Mokhtar. morad.mokhtar@ageri.sci.eg   link