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Old 11-30-2014, 03:38 AM   #1
angel-sakura
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Location: Aus

Join Date: Nov 2014
Posts: 23
Default how to visualize locations of lncRNA close to my gene of interest

Hi, everyone, I am looking for the lncRNAs of some specific genes.
Q1: Now I have extracted all predicted lncRNAs (using PLEK) that close to my target genes (500 KB upstream or downstream). I can do blastn to get the location of those lncRNAs on gene scaffold I extracted from genomic sequence (my target gene +/-500KB). But I don't know how to visualize them. Could someone please show me the software or protocol?
Q2: Is there any lncRNA database or lncRNA database with consensus sequences that I can blast with?
Q3: Is there any software or command that I can predict structure/function/lncRNA-protein, lncRNA-DNA,lncRNA-microRNA interaction of lncRNAs (with multiple sequences as input)?

Thank you very much!
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