ORFfinder length filter
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5 days ago
Princy ▴ 40

Hi, How to find transcript less than equal to 300 bp ORF length from ORFfinder result. my output is like this

>lcl|ORF1_TRINITY_DN317904_c0_g1_i1:141:245 unnamed protein product 
 MYNCYYVIVFKCNFLSCSCFKQFFVMKLLLNYSF 
>lcl|ORF2_TRINITY_DN317904_c0_g1_i1:34:165 unnamed protein product
 MKKTSYNTFICHEKKSVEVLCHKVVTVTIFNGHNYFCIIVTTL

and why do we need to discard more than 300 bp ORF length to find the lncRNA?

Filter ORFfinder • 304 views
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remember: lnc stands for Long-Non-Coding. Such sequence should not code for polypeptide. Possibly, this is the reason why one might discard lncRNA candidates that contain long ORFs and thereby might look like protein coding genes, but that isn't much more than a rule of thumb I guess.

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