LncSeeker: A web-server to process transcriptome annotation profiles generated by RNA-seq.

Upload Data:

1. Choose Reference Genome:

2. Enter transcript data ( BED12 / GTF )

Load transcript data ( BED12 / GTF )

Example BED File (Human) Example GTF File (Human)

3. Input your email address (Optional):

Optional Parameters:

remove transcripts with length < =

remove transcripts with exon number < =

remove transcripts with ORF length (Amino Acid) > =

remove transcripts with ORF Coverage>=

remove transcripts with ORFScan score >=

remove transcripts overlapped with exons of protein-coding genes:

ucsc Protein   refGene Protein    Ensembl Protein

remove transcripts overlapped with known non-lncRNAs:

GENCODE other ncRNAs

remove transcripts overlapped with exons of pseudogenes:

GENCODE pseudogene

remove transcripts with HMMER databases (Pfam) E-value <

remove transcripts mapped to unitRef90 database with BlastX E-value<=

  • We provide a web-based tool named IncSeeker to implement our filtering pipeline of finding lncRNAs transcriptome assembled from RNA-seq data.

  • Users can upload their transcriptome data in BED12 or GTF format (usually assembled by Tophat and Cufflinks ), and our web-server will process the file by a series of tunable criterion and filter steps, including transcript length, exon number, coding ability and potential coding domain.

  • A set of highly credible lncRNAs will then be displayed on the result page.