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