Question: I am trying to write a code to compare some covid samples but I am getting a syntax error on: print('Total proteins:', len(df))def conv(item): I tried to add “()” and change some def in the code but I keeps ...

Question: I am doing simply queries on a csv document about a genome. I have the following code: That gives me the following sequence: I also have the following code that is supposed to give me the same exact sequence: ...

Question: I have a pandas dataframe that contains DNA sequences and gene names. I want to translate the DNA sequences into protein sequences, and store the protein sequences in a new column. The data frame looks like: DNA gene_name ATGGATAAG ...

Question: Both degeneracy1 and protein_ls are not being reassigned in the nested while loops I am using, I can’t figure out why this. This program is designed to find the best protein motif to create an oligo for genetic engineering. ...

Question: I have asked a question on another platform (here) – it would be great to get your input in order to make my Python code run in a very short time. Currently, it has been taking more than 3 ...

Question: I have an almost similar question to the topic : https://www.biostars.org/p/154993/ I have a fasta file with align sequence and I want to generate a consensus by using IUPAC code. So far I wrote : The “0.3” is the ...

Question: I have a phylogenetic tree in Newick format. A sample from the full string looks like this: “…(tet_rpg.hmm_GCA_000638155.1_seq1:0.001565531,tet_rpg.hmm_GCA_000507745.1_seq1:0.001565235)0.000:5e-09,…”. I understand that distances are given by the number after a colon, but what do numbers immediately following closed parentheses signify? ...

Question: I am working on Next Generation Sequencing (NGS) analysis of DNA. I am using SeqIO Biopython module to parse the DNA libraries in Fasta format. I want to filter the unique clones (unique records) only. I am using the ...

Question: I have been sorting through a ~1.5m read fasta file (‘V1_6D_contigs_5kbp.fa’) to determine which of the reads are likely to be ‘viral’ in origin. The reads in this file are denoted as Vx_Cz – where x is 1-6, depending ...

Question: I want to do continuous renumbering a pdb file having multiple chains(A,H,L). Some of the chains have insertion codes attached to the residue position (e.g., 190A etc.). Can anybody help me how to write this code? Example of pdb ...