Tag: .Gbk

Solved In this problem, we will use Biopython to translate

In this problem, we will use Biopython to translate the CDS (CoDing Squence) sequence(s) in GenBank file. First, use the retrieve_GenBank_info(id) (from the lecture notw, also given below) to save the GenBank record of Helicobacter pylori 26695. id is the id of helicobactor you found in Problem 3. Make sure…

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Solved Problem 2 In the class, we wrote a function

Problem 2 In the class, we wrote a function retrieve_GenBank_info(id) that retrieves a sequence information in the GenBank format from NCBI, saves it into a file, and returns the requence. In this problem, your task is to convert this function to retrieve_FASTA_info(id) that retreives a sequence in the fasta format,…

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Whole Plasmid Sequencing Details

Sample Preparation Sample type Size Category Length Concentration Min volume Price per sample Plasmid Regular 2.5 – 25 kb 30 ng/uL ≥10 uL $15 Large 25 – 125 kb 50 ng/uL ≥20 uL $30 XL 125 – 300 kb 50 ng/uL ≥40 uL $60 Linear/Amplicon Standard 600 bp – 25…

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Database from .gbk files

Database from .gbk files 1 Hello all, I would like to use a relatively old program called MultiGeneBlast (from 2015) to do some work. The database packaged with this software is also from 2015 and since then, I believe there are a lot more bacterial genomes on the ncbi website….

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Mac program for DNA analysis and cloning.

Tool:BioLabDNA – Mac program for DNA analysis and cloning. 0 BioLabDNA is one time purchase program with lifetime updates including new features. This program is aimed at researches in the molecular biology field. BioLabDNA is the document based app focused on the analysis and manipulation of DNA sequences. The user…

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how to extract specific region in genbank file (.gbk)

how to extract specific region in genbank file (.gbk) 2 In the “genbank file” posted on ncbi, “Change region show” allows features of a specific location to be extracted into a gbk file. In addition, the positions of the extracted features count from 1. EX) raw. gbk – gene A…

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cblaster didn’t create .dmnd out file???????

cblaster didn’t create .dmnd out file??????? 0 Hi, i am running cblaster and it didn’t create .dmnd diamond, however it only create sqlite3 and fasta file. if anyone know anything please let me know. It will be great help. cblaster makedb -n localD -f $(ls ~/Neelam/43_strains_gbk/*.gbk) [18:20:39] INFO – Starting…

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Append assembly accession to nucleotide accession number in RefSeq Genbank file

Append assembly accession to nucleotide accession number in RefSeq Genbank file 0 Hi everyone, When I want to append the filename to the contig header in a multi-fasta file, I usually use for F in *.fasta; do N=$(basename $F .fasta) ; bbrename.sh in=$F out=${N}_mod.fasta prefix=$F addprefix=t ; done However, this…

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How To Download .Gbk Files From Ncbi Website

How To Download .Gbk Files From Ncbi Website 1 how to download .gbk files from ncbi website? ncbi download genbank • 25k views • link updated 38 minutes ago by Ram 34k • written 9.8 years ago by Arun • 0 Search for the sequence that you want. The “display…

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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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New Mac program for molecular biologists

Tool:New Mac program for molecular biologists 12 I would like to present here a program – BioLabDonkey – for molecular biologists who are Mac users. This program is written from scratch in a language native for Mac – Swift. The program can be downloaded from mac App Store – apps.apple.com/us/app/biolabdonkey/id1470827582?ls=1&mt=12…

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