ORFfinder length filter
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?
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Michael Dondrup
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Princy •
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Princy •
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How To Filter Multi Fasta By Length??
Remove sequences <300 bases from FASTA file
Filter DNA sequence in FASTA file by minimum length and redirect sequences that don't meet condition to new file using python
How to extract sequences from fasta that have a certain length ?
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.