User: swknudsen

gravatar for swknudsen
swknudsen40
Reputation:
40
Status:
New User
Location:
Last seen:
2 years, 7 months ago
Joined:
2 years, 7 months ago
Email:
s********@snm.ku.dk

Posts by swknudsen

<prev • 6 results • page 1 of 1 • next >
1
vote
1
answer
4.3k
views
1
answers
Comment: C: Splitting and Extracting Features in fasta format from Genbank Files using Biopy
... Yes. This is it. Thank you so much for the last piece of code: extractNAfeatures.py. I checked a couple of the resulting nd6-genes in the mt-genome. They appear to be on the same strand as the other ones I have from my assembled mt-genomes. The genes on the forward strand also appear to match the re ...
written 2.6 years ago by swknudsen40 • updated 2.6 years ago by WouterDeCoster40k
0
votes
1
answer
4.3k
views
1
answers
Comment: C: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
... Oh. No. This was not what meant. I am fully aware that I cannot retro-translate. I am aware of the redundancy in the AA-translation code. Retro translation is certainly not the idea. As a full scale phylogenetic analysis is the ultimate goal further down the line, I need the original nucleotide dat ...
written 2.6 years ago by swknudsen40
0
votes
1
answer
4.3k
views
1
answers
Comment: C: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
... Brilliant this almost works. With a bash-code on the side I was able to move the resulting files forth and back. Just one thing is missing. The # genbank2fasta.py part produces the '.faa'-files with amino-acid codes in fasta-format. I would prefer to have nucleotide information in the resulting '.fa ...
written 2.6 years ago by swknudsen40
1
vote
1
answer
4.3k
views
1
answers
Comment: C: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
... I prepared the multi-gbk with this: from Bio import Entrez Entrez.email = "myemail@email.com" f1 = open("/home/forbio/python_test_2016/tobis_list_of_acc_no_shortlist.txt") f2 = open('tobis_list_of_acc_no_shortlist.gbk', 'w') for line in iter(f1): handle = Entrez.efetch( ...
written 2.6 years ago by swknudsen40 • updated 2.6 years ago by genomax70k
0
votes
1
answer
4.3k
views
1
answers
Comment: C: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
... Yes. I have a gbk-file with 200 full genbanks in it. Here is an example with 3 full genbanks in it. https://www.dropbox.com/s/7fu69897ua66voh/tobis_list_of_acc_no_shortlist.gbk?dl=0 This is a gbk-file for the 3 accession numbers: NC_010689, NC_015654 and NC_026578 I do not want the full fasta-seque ...
written 2.6 years ago by swknudsen40
9
votes
1
answer
4.3k
views
6 follow
1
answer
Splitting and Extracting Features in fasta format from Genbank Files using Biopython
... With a genbank file (tobis_list_of_acc_no.gbk) that contains full mitochondrial genomes for 200 mitochondrial genomes, I would like to obtain fasta-files (one for each genome), but with the the fasta-sequences in each of the files parsed into individual fasta-sequences for each gene in the mitochond ...
gene genome sequence written 2.6 years ago by swknudsen40 • updated 2.6 years ago by WouterDeCoster40k

Latest awards to swknudsen

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1524 users visited in the last hour