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Genoscope's bioinformatics resources

Published on 20 November 2018

MicroScope platform

The platform for annotation and comparative analyses of prokaryote genomes developed by the Laboratory of Bioinformatics Analyses for Genomics and Metabolism: the MicroSc​ope platform (MaGe). The IT infrastructure incorporates the data (genomes, automated and expert annotations, results of analyses and experimental data) and Web graphic interfaces enabling exploration of the data and use of the methodological tools regularly incorporated on the platform.



Bioinformatics developments

  • Nanopore Synthetic Long-Reads (NaS) is a hybrid approach under development at Genoscope with a view to exploiting the data generated by the MinION sequencer. We are combining Illumina and Oxford Nanopore technologies to produce error-free long synthetic reads.
  • TE-Tracker is a program for detection of structural variations used, in particular, to study the mobility of transposons in Arabidopsis.
  • MaGuS is an evaluator, without any reference, of assembly quality and a map-guided scaffolder based on a physical map and Illumina-type sequencing data.​

Human genetic map, additio​nal data ​(Nature 1996)

This table provides direct access to tabular data and chromosome maps related to this publication :

Dib C. et al, A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380, 152 - 154 (14 March 1996); doi:10.1038/380152a0. 
Abstract | PDF (Links to the Nature Website ; full text (PDF document) may require special arrangment with Nature Publishing Group).​

Chromosomes

Alleles

Data

Chromosome map (PDF format)

sequences

Chr1

Allele Chr1

Data Chr1

Figure Chr1

Sequence Chr1

Chr2

Allele Chr2

Data Chr2

Figure Chr2

Sequence Chr2

Chr3

Allele Chr3

Data Chr3

Figure Chr3

Sequence Chr3

Chr4

Allele Chr4

Data Chr4

Figure Chr4

Sequence Chr4

Chr5

Allele Chr5

Data Chr5

Figure Chr5

Sequence Chr5

Chr6

Allele Chr6

Data Chr6

Figure Chr6

Sequence Chr6

Chr7

Allele Chr7

Data Chr7

Figure Chr7

Sequence Chr7

Chr8

Allele Chr8

Data Chr8

Figure Chr8

Sequence Chr8

Chr9

Allele Chr9

Data Chr9

Figure Chr9

Sequence Chr9

Chr10

Allele Chr10

Data Chr10

Figure Chr10

Sequence Chr10

Chr11

Allele Chr11

Data Chr11

Figure Chr11

Sequence Chr11

Chr12

Allele Chr12

Data Chr12

Figure Chr12

Sequence Chr12

Chr13

Allele Chr13

Data Chr13

Figure Chr13

Sequence Chr13

Chr14

Allele Chr14

Data Chr14

Figure Chr14

Sequence Chr14

Chr15

Allele Chr15

Data Chr15

Figure Chr15

Sequence Chr15

Chr16

Allele Chr16

Data Chr16

Figure Chr16

Sequence Chr16

Chr17

Allele Chr17

Data Chr17

Figure Chr17

Sequence Chr17

Chr18

Allele Chr18

Data Chr18

Figure Chr18

Sequence Chr18

Chr19

Allele Chr19

Data Chr19

Figure Chr19

Sequence Chr19

Chr20

Allele Chr20

Data Chr20

Figure Chr20

Sequence Chr20

Chr21

Allele Chr21

Data Chr21

Figure Chr21

Sequence Chr21

Chr22

Allele Chr22

Data Chr22

Figure Chr22

Sequence Chr22

ChrX

Allele ChrX

Data ChrX

Figure ChrX

Sequence ChrX​




Bioinformatiques resources​

The bioinformatics resources for organisms are of several types:

  1. Blast  for Basic Local Alignment Search Tool:  method for comparison of DNA or protein sequences.
  2. GGB for Generic Genome Browser (Article):  graphic interface for various databases (sequence, annotation, synteny, etc.) for an organism. ​


​​​If you have questions on Genoscope's GGB:   

ggbcnsgenoscope.cns.fr


​​Arabidops​​is thal​iana


​ Classification eudicotyledons
​Publica​​tions​2000, 2004
​Project ID​-​
​Accession Number​-​
​Taille assemblage​-
​Nb Genes​-
​GGB​

​Homo sapiens


Classification Mammalia
​Publications​2003, 2006​
​Project ID​PRJNA31257
​Accession Number​
​Taille assemblage​
​Nb Genes​
​GGB​K14, Alternative splicing

​​​Oikopleura dioica
 


Classification Tunicata
​Publications​2010
​Project ID​PRJNA12901
​Accession Number​CABV00000000.1
​Taille assemblage​70 Mb
​Nb Genes​18,02
​GGB​Serv​eur Blat
​Assemblage​Gen​es

​​Paramecium tetraurelia
​


Classification Ciliophora
​Publications​2006
​Project ID​PRJNA18363
​Accession Number​CAAL00000000.1​
​Taille assemblage​72 Mb
​Nb Genes​39,642
​GGB​Serveur Blat
​Assem​blage ​Genes


​Tetraodon nigroviridis
 



Classification 
Vertebrata
Publications 2004
Project ID PRJNA12350
Accession Number CAAE00000000.1
Taille assemblage342 Mb
Nb Genes27,918
GGB Serveur Blat
Assemblage Genes


​​Vitis vinifera
 

​​​
Classification eudicotyledons
Publications 2007
Project ID PRJEA18785
Accession Number CAAP00000000.3
Taille assemblage486 Mb
Nb Genes26,346
GGB Serveur Blat
Assemblage​​Gen​es

​​Tuber melanosporum
 

Classification Ascomyta
​Publications ​2010
​Project ID​PRJEA38847
​Accession Number​CABJ00000000.1
​Taille assemblage​7,496
​Nb Genes​125 Mb
​GGB​​Serveur Blat
​Assemblage​Genes


​​
Blastocystis hominis










Classification Stramenopiles
​Publications 2011
​Project ID​PRJEA45923
​Accession Number​CABX00000000.1
​Taille assemblage​19 Mb
​Nb Genes​6020
​GGB​Serveur Blat
​Assemblage​Genes
​​



​Chondrus crispus




Classification Rhodophyta
Publications 2013
Project ID PRJEA78309
Accession Number CAKH00000000.1
Taille assemblage105 Mb
Nb Genes9,807
Assemblage Genes



Babesia microti
 

​Classification Apicomplexa
Publications 2012
Project ID PRJEA72411
Accession NumberFO082871.1, FO082872.1, FO082874.1, FO082868.1
Taille assemblage6 Mb
Nb Genes1,426
Assemblage Genes
​​
Phytomonas sp. (isolate EM1)


Classification Phytomonas
​Publications​2014
​Project ID​PRJEB1535
​Accession Number​CAVQ000000000.1
​Taille assemblage​18 Mb
​Nb Genes​6,381
​GGB​Serveur Blat
​Assemblage​Genes


​Phytomonas sp. (isolate HART1)


Classification Phytomonas
​Publications​2014
​Project ID​PRJEB1535
​Accession Number​CAVR000000000.2
​Taille assemblage​18 Mb
​Nb Genes​6,451
​GGB​Serveur Blat
​Assemblage​Genes​


​Musa acuminata



Classification Liliopsida
​Publications​2012
​Project ID​PRJEA82777
​Accession Number​CAIC00000000.1
​Taille assemblage​472 Mb
​Nb Genes​36,542
​Assemblage​Genes


​Brassica napus




Classification eudicotyledons
​Publications​2014
​Project ID​PRJEB5043
​Accession Number​CCCW000000000.1
​Taille assemblage​848 Mb
​Nb Genes​101,04
​GGB​Serveur Blat
​Assemblage​Genes

​​Adineta vaga








Classification Rotifera
​Publications​2013
​Project ID​PRJEB1171
​Accession Number​CAWI000000000.2
​Taille assemblage​218 Mb
​Nb Genes​49,3
​GGB​Serveur Blat
​Assemblage​Genes

​Oncorhyncus mykiss​


Classification Vertebrata
​Publications​2014
​Project ID​PRJEB4421
​Accession Number​CCAF000000000.1
​Taille assemblage​1.9 Gb
​Nb Genes​46,585
​GGB Serveur Blat
​Assemblage​Genes

​



Coffea canephora​


Classification eudicotyledons
Publications 2014
Project ID PRJEB4211
Accession Number CBUE0​00000000.2
Taille assemblage570 Mb
Nb Genes25,574
Assembly​ Genes

Kuraishia capsulata​





Classification 
Ascomycota
Publications 2013
Project ID PRJEB4427
Accession Number CBUD000000000.2
Taille assemblage11 Mb
Nb Genes6,029
Assembly Genes

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