Tag: antiSMASH

biopython – Parsing a gene bank file and outputting specific feature information to a csv using Bio Python

So I am trying to parse through a gene bank file, extract particular feature information and output that information to a csv file. The example gene bank file looks like this: SBxxxxxx.LargeContigs.gbk LOCUS scaffold_31 38809 bp DNA UNK 01-JAN-1980 DEFINITION scaffold_31. ACCESSION scaffold_31 VERSION scaffold_31 KEYWORDS . SOURCE . ORGANISM…

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Postdoctoral Research Associate – Bioinformatics in Boston, MA for Northeastern University

Details Posted: 13-Jul-22 Location: Boston, Massachusetts Type: Full-time Salary: Open Postdoctoral Research Associate – Bioinformatics About the Opportunity We are seeking a creative scientist with a background in computational biology and microbiology to work on a genomics analysis-based antibiotic discovery project. The successful applicant will join a team of talented…

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Postdoctoral Research Associate – Bioinformatics job with Northeastern University

Postdoctoral Research Associate – Bioinformatics About the Opportunity We are seeking a creative scientist with a background in computational biology and microbiology to work on a genomics analysis-based antibiotic discovery project. The successful applicant will join a team of talented researchers at the Antimicrobial Discovery Center. Several drug lead candidates…

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Bacterial endosymbionts protect beneficial soil fungus from nematode attack

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

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parsing gbk files (antismash result)

parsing gbk files (antismash result) 0 Hello I used antismash from the CLI and I got 700 gbk files (1 gbk file per each analyzed genome). I used the following script to retrieve the predicted products from the gbk files: from Bio import SeqIO import glob for files in glob.glob(“*.gbk”):…

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antiSMASH output

antiSMASH output 0 Hello. Can someone help me to interpret the antiSMASH output and the count number of BGCs by using command line. It would be great to receive your help. Thank you RESULTS antiSMASH • 65 views Login before adding your answer. Source link

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STAR rna-seq for bacterial genomes

Hi, I’m willing to use STAR for bacterial genomes. I wanted to ask if this is strongly unadvised or if there is a way to manage the main challenges of mapping reads to prokaryotes. (I know there are specific tools for this purpose, i.e. EdgePro, but I’m a beginner in…

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