Deinococcus radiodurans R1 [deep sequencing]

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UMR C8621 Centre Universitaire d'Orsay Batiment 400,
Orsay France


Sequence info: 03/25/15 from WGS LOCUS JHYL01 01-51
biological samples from S. Sommer's lab / Deinococcus radiodurans R1 stationnary & exponential phases
raw data : Imagif / Illumina HiSeq
assembly BAM2 = bwa/samse v0.6.2 (imagif)
assembly MEM = bwa/mem v0.7.9a (yz)
reference strain = Deinococcus radiodurans R1 Acc# NC_001263, NC_001264, NC_000958, NC_000959
variant calling = VarScan.v2.3.6
Last modification: Wed Aug 07 2024 17:48:41
      
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sequences and definitions 		Database/link Status  
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Separate gene names by: space, "," ,";", tab, return. !! Character case is important !!
(e.g. :DRA1_stat1_mem_2208 DRA1_stat2_mem_2209 DRA1_expo1_bam2_2210)
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D.radiodurans wgs + ds /mem pseudo
2 chromosomes + 2 plasmids
DRAD WGS
 Open  
 
D.radiodurans ATCC BAA-816
 2 chromosomes + 2 plasmids
D.radiodurans ATCC BAA-816
 Open  
 
D.radiodurans R1 CP015081 (HUA)
 2 chromosomes + 2 plasmids
D.radiodurans R1 (HUA)
 Open  
  Blast search: Blast in DRA WGS_Deep_Sequencing sequence databases Open  
  DRA_WGS_DS gene cross reference with D. radiodurans & D. radiodurans R1 HUA(1) best match of DRA R1 genes in DRA_WGS_DS gene pool Open  
  DRA_WGS_DS gene cross reference with D. radiodurans & D. deserti(1) best match of DRA R1 genes in DRA_WGS_DS gene pool Open  
  DRA_WGS_DS gene cross reference with D. radiodurans & D. gobiensis(1) best match of DRA R1 genes in DRA_WGS_DS gene pool Open  
  DRA_WGS_DS <==> D.rad R1 Differences (2) COMPLETE SNPS & INDELs DRA_WGS_DS/ DRAR1 COMPARISON Open  
  DRA_WGS_DS // D.rad R1 CP015081 (HUA) Differences DRA_WGS_DS/ D.radiodurans R1 CP015081 (HUA) COMPARISON ELEMENTS Open  
  DRA_WGS DEEP sequencing COVERAGE coverage graphs for chromosomes 1,2 & pMP1 plasmid Open  
  Regulatory patterns finder Find location of nucleotidic patterns in genomic data Open  
  Annotation Database: Available annotations & more in DRA_DS database Open  
   Matched Database Search Form: RefSEq + CDD + COG + INTERPRO similarity/motif search results Open  
  Genome Guts : retrieve genome sequences and inner parts Open  
   Nucleotidic sequence: retrieve complete sequences Open  
   Gene's sequences (amino): Retrieve gene's sequences Open  
  Genes sequences (nucleic): retrieve gene's sequences Open  
  START CODONS prodigal PREDICTED CDS start codons in orfs context Open  
  WGS SCAFFOLD GAPS FILLING Gaps in WGS scaffold filled with D. radiodurans R1 sequence Open  
  RNASeq Time course RNASeq data : 17357/17370 Time course / DESeq statistical analysis Open  
  D. radiodurans 3 genomes cross-reference and gene info retrieval Quick & easy info retrieval Open  
  D. radiodurans resequencing D.rad Illumina & nanopore resequencing stuff Open  
  (1) dra_wgs_ds homologs in DRA R1 identified by match in RefSeq DB
(2) complete position specific snps & indels comparison 		 
     
 

Problems/Questions: yvan.zivanovic@u-psud.fr