Stack Overflow
Stack Overflow

Questions tagged [genbank]

GenBank format (GenBank Flat File Format) consists of an annotation section and a sequence section. The start of the annotation section is marked by a line beginning with the word "LOCUS".

GenBank format (GenBank Flat File Format) consists of an annotation section and a sequence section. The start of the annotation section is marked by a line beginning with the word LOCUS.

53 questions
0
votes
1 answer

Please help me to read a genbank file from disk and convert it to fasta

Please guide me to convert a GenBank sequence to its equivalent FASTA format using biosmalltalk (Pharo edition). I have already figured out to read a GenBank file from disk: | file x y m | x:=Time millisecondClockValue . file := BioFile on:…
Dip Moitra
  • 11
  • 2
0
votes
1 answer

Biopython parsing a GBK file without genome sequence

I wrote a script that uses a GenBank file and Biopython to fetch the sequences of given genes from the sequence part of the GBK file, which my colleagues use for their work. We had some problems now with a new data set, and it turned out that the…
Lilith-Elina
  • 1,613
  • 4
  • 20
  • 31
0
votes
1 answer

SeqIO: "no records found in handle"

I'm just getting started with Python and BioPython and don't have too much programming experience. I'd appreciate any help you guys could give me. I'm trying to extract CDS and/or rRNA sequences from genbank. It's important that I'm only getting…
jrp355
  • 83
  • 8
0
votes
1 answer

Python. Trying to sort a file for 3 longest gene nucleotide sequences from genbank file into fasta file using BioPython

I am relatively new to python so please forgive the idiocies that come with this question. I have a genbank file and have written a piece of code that will take the top 3 longest genes and place them into a newly generated fasta file. from Bio…
Peepo
  • 3
  • 2
0
votes
2 answers

Parsing GenBank file: get locus tag vs product

Basically, a GenBank file consists on gene entries (announced by 'gene' followed by its corresponding 'CDS' entry (only one per gene) like the two I show here below. I would like to get locus_tag vs product in a tab-delimited two column file. 'gene'…
biotech
  • 697
  • 1
  • 7
  • 17
0
votes
1 answer

pull out sequence from genbank formt

This code was working properly but now it complains, does the genbank structure changed? #!/usr/bin/perl -w …
user1876128
  • 91
  • 14
-1
votes
1 answer

Loop through files in a directory with python

I have written a python function which will take a single genbank file and pull the nucleotide sequences out, writing it over the original file.. from Bio import SeqIO from Bio.SeqRecord import SeqRecord _Sequences = [] def func(file): for rec…
Taliamycota
  • 125
  • 7
-1
votes
1 answer

Getting protein FASTA sequence based on keyword with python

I would like to gather proteins FASTA sequence from Entrez with python 2.7. I am looking for any proteins that have the keywords: "terminase" and "large" in their name. So far I got this code: from Bio import Entrez Entrez.email =…
tahunami
  • 141
  • 1
  • 7
1 2 3
4