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ALDB: a domestic-animal long noncoding RNA database
Introduction
The domestic-animal lncRNA database (ALDB) is the first comprehensive database with a focus on the domestic-animal lncRNAs. ALDB currently comprises 12,103 pig lincRNAs, 8,923 chicken lincRNAs, and 8,250 cow lincRNAs, which we have identified using computational pipeline in this study. Moreover, ALDB provides related useful data, such as genome-wide expression profile and animal quantitative trait loci (QTLs), that is not available in the existing lncRNA database (lncRNAdb and NONCODE), along with convenient tools, such as BLAST, GBrowse and flexible search functionalities.
This published compressed file(.zip) includes the following files:
Pig (Sus scrofa) lincRNAs
Pig lincRNAs (on SS_10.2 in GFF3 format)
Pig lincRNAs (on SS_10.2 in GTF format)
Pig lincRNAs (in fasta format)
Pig lincRNAs (on SS_10.2 in GTF format) [Identified by Zhou et al. ]
Chicken (Gallus gallus) lincRNAs
Chicken lincRNAs (on GG_4.0 in GFF3 format)
Chicken lincRNAs (on GG_4.0 in GTF format)
Chicken lincRNAs (in fasta format)
Cow (Bos taurus) lincRNAs
Cow lincRNAs (on UMD_3.1 in GFF3 format)
Cow lincRNAs (on UMD_3.1 in GTF format)
Cow lincRNAs (in fasta format)
Pig (Sus scrofa) expression
Pig FPKM expression levels, derived from ERA178851 using TopHat and Cufflinks
Pig count expression levels, derived from ERA178851 using SummaryOverlaps
Chicken (Gallus gallus) expression
Chicken FPKM expression levels, derived from SRA059960 using TopHat and Cufflinks
Chicken count expression levels, derived from SRA059960 using SummaryOverlaps
Cow (Bos taurus) expression
Cow FPKM expression levels, derived from SRA059960 using TopHat and Cufflinks
Cow count expression levels, derived from SRA059960 using SummaryOverlaps
CNCI of lincRNA transcripts
ALDB_pig_lincRNAs_with_CNCI
ALDB_chicken_lincRNAs_with_CNCI
ALDB_cow_lincRNAs_with_CNCI