Databases available for ViroBLAST

Nucleotide sequence databases (last update: 2019-DEC-10)

 

Lo7 WGS contigs v2 = "RYE-SELECT Lo7 WGS contigs version 2"
   N50: 233,728
   L50 [bp]: 1,708
   number of contigs: 1,581,707
   contig size [bp]: 1,684,931,674
   largest contig [bp]: 35,334

 

Lo7 gene models v3 [CDS] = "RYE-SELECT Lo7 gene models version 3"
   N50: 6,664
   L50 [bp]: 1,239
   number of sequences: 27,784
   sequence size [bp]: 25,846,026
   largest gene [bp]: 15,366

 

RYE-EXPRESS Sce_Assembly02 = "RNA-seq contigs v1 (reference for SNP discovery), DOI: 10.1186/1471-2229-11-131"
   N50: 31,409
   L50 [bp]: 425
   number of contigs: 138,339
   contig size [bp]: 54,456,665
   largest contig [bp]: 7,289

 

RYE-EXPRESS Sce_Assembly03 = "RNA-seq contigs v1 (transcriptome reference), DOI: 10.1186/1471-2229-11-131"
   N50: 24,496
   L50 [bp]: 623
   number of contigs: 115,400
   contig size [bp]: 56,598,912
   largest contig [bp]: 8,636

 

TrSc4B Trinity = "TrSc4B_Trinity.fasta"
Number of contigs: 87,987 - Dataset for research of B-chromosomes.

 

Anth 4B Trinity = "Anth_4B_Trinity.fasta"
Number of contigs: 81,209 - Dataset for research of B-chromosomes.

 

Trinity assembly 0B = "All RNASeq contigs from rye with 0Bs"
Number of contigs: 107,534; Contig size: 103,393,860 bp; N50: 1,614 - Dataset for research of B-chromosomes.

 

"All_Contigs_from_sorted_Rye_B_chromosoms_HMGU"
Assembly results computed at the HMGU for the dataset: All Reads from sorted Rye B chromosomes.

 

Trinity assembly 4B = "All RNASeq contigs from Rye with 4Bs"
Number of contigs: 141,311; Contig size: 147,256,790 bp; N50: 1811 - Dataset for research of B-chromosomes.

 

Amino acid sequence databases (last update: 2019-DEC-10)

 

Secale_cereale_Lo7_2018v1p1p1.pgsb.Feb2019.HC.aa.fasta = "Sequence for all high-confidence annotated gene-related features, DOI: eDal repository"
   mean length [bp]: 24,496
   number of contigs: 34,441
   contig size [bp]: 14,727,541
   largest contig [bp]: 5,358

 

Secale_cereale_Lo7_2018v1p1p1.pgsb.Feb2019.all.aa.fasta = "Sequence for all low-confidence annotated gene-related features, DOI: eDal repository"
   mean length [bp]: 428
   number of contigs: 34,441
   contig size [bp]: 19,555,688
   largest contig [bp]: 5,358

 

 

Lo7 proteins v3 [PEP] = "RYE-SELECT Lo7 gene models version 3"
   N50: 6,664
   L50 [aa]: 413
   number of proteins: 27,784
   sequence size [aa]: 8,615,342
   largest peptid [aa]: 5,122