ALDB: a domestic-animal long noncoding RNA database

2015-03-03T02:03:11Z (GMT) by Aimin Li

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