ORFfinder length filter

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2.5 years ago

Princy ▴ 60

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 • 1.2k views

ADD COMMENT • link updated 2.5 years ago by Michael 55k • written 2.5 years ago by Princy ▴ 60

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How To Filter Multi Fasta By Length??

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 164k

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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.

ADD REPLY • link 2.5 years ago by Michael 55k

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Remove sequences <300 bases from FASTA file

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 164k

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Filter DNA sequence in FASTA file by minimum length and redirect sequences that don't meet condition to new file using python

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 164k

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How to extract sequences from fasta that have a certain length ?

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 164k