Questions tagged [orf]

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1 answer

How to tackle an Index Error in my code for finding ORFs

I have created a python code that prints out all lengths of ORFs in a DNA sequence (start codon - "ATG", stop codons - "TAG", "TAA" and "TGA". It seems to give ...
3 votes
2 answers

How to convert Sars-CoV-2 ORF1ab codon positions to ORF1b positions?

Some websites mention amino acid mutations as ORF1ab, most however use ORF1a/b instead. So how can I translate from one to the other? What do I need to subtract from say ...
1 vote
0 answers

Prokka error message

I am trying to run Prokka but the following error message appears: Could not run command: makeblastdb -hash_index -dbtype prot -in /cluster/software/prokka/1.13.7-gompi-2019a/db/kingdom/Archaea/sprot ...
2 votes
0 answers

How to extract Genbank sequence and identify ORFs from the sequence in R?

I used ape::read.GenBank and then used the function ORFik::findORFs to find ORFs in the sequence of interest. But the former ...
1 vote
1 answer

Bedtools get fasta and ORF from a blastX run

Hello I made a blastX research (A query genome in nucleotide format translated into protein in 6 reading frames against a protein dabatase) And here is a head of ...
0 votes
1 answer

how to Know the longest ORF in Protein?

I have a protein Seq. and I want to know how to Know the longest ORF in this Protein? and if there is any tutorial for this process ??