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• Writing Genbank files
  Hi all, I have information about a gene stored in a Python Class as shown below class Gene(...
• Get location based on protein ids from genbankfile
  Hello everyone.. I am quite new in here also with biopython. I have a set of protein ids, using ...
• How To Extract Rrna Sequences (In Fasta Format) From Genbank (Bacterial Genome)?
  In the genbank files rRNA only have following features to it: rRNA 67149..68657...
• Extract old_locus_tag information from genbank files
  Hi,  I have a python script that allows me to extract the locus_tag info from a genbank file but...
• Error Translating Genbank Cds Using Biopython
  Hi all, I'm trying to translate the a genbank record using BioPython 1.53, ignoring the already ...
• Gff Converter For Use With Mummer/Promer (Microbial Genome)
  Hi, Does anyone of a script to convert a gff3 file into a format that PROmer's mapview can accep...
• Extracting strings from the fasta header
  I want to extract **gene name** , **gene start position** and **gene stop position** from the fas...
• How to parse protein and dna sequences from prokka generated gbk or gff file based on locus_tag?
  I need to parse `accessory gene sequences (both dna and amino acid sequences)` from `roary pangen...
• To compare two genes from different species from a .gbff
  I'm trying to compare two genes from different species using a genbank file (gbff), but I'm not s...
• Genes On Gi Sequences From Ncbi
  I am looking for a comprehensive list of gene positions on GI sequences. I have found gene2access...
• duplicating features in genbank file with biopython
  I have got a lot of genbank files with multiple genes in them, some of these genes have a single ...
• Extract protein sequences or names based on GFF and protein file
  Dear all, In short, my gene ID's of the gff file do not correspond with the protein headers whil...
• [Title Edited] How to update the GFF3 wrong file? [was:] featureCounts may be ignore chloroplast sequences in a plant genome when use -t exon and -g ID in a GFF file?
  I run featureCounts like this: featureCounts -p -F GFF -a ./NCBI/GCF_000612305.1_Egrandis1_0...
• Extracting exons from CDS CompoundLocations of a genbank file
  Hi all,  Using biopython, I'm dealing with a genbank file that only has CDS annotated as feature...
• Extracting Specific Regions In Genbank File
  I have the following file format: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord#FeaturesA and...
• Empty in genebank extractor python code
  I found the gbk extractor python code here (https://github.com/LiguanLi/ARG_MRG_Cooccurrence/blob...
• split a GFF3 with many Genomes to GFF3 files with individual Genomes
  Hi all, I have a big GFF3 file that I downloaded from Batch Entrez and it contains 54 genomes. I ...
• genbank parsing using perl
  I have genbank file. and want to retrieve relevant information. the problem is when the code fetc...
• Multi-records genbank to CDS
  Hi! I have a file containing several genebank records written one after the other. I need to extr...
• More file parsing :) ***EDIT*** how do I make a fast and bed file from Genbank file - SOLVED
  Hi All,  I'm trying to make a script that will allow me to take a given genbank file and convert...
• Fasta extraction from bed file
  hello, how can i extract fasta in reverse order. i have bed file where start position is great...
• Retrieve multi-line fasta sequences using list of locus tag
  Dear all Can someone tell me how to retrieve multi-line fasta file from for instance below mentio...