Search engine for discovering works of Art, research articles, and books related to Art and Culture
Javascript must be enabled to continue!
Bacterial genome annotation script using BLASTN v2
View through CrossRef
This protocol uses a python based script and command-line BLASTn to annotate in a final table single-read sequencing results from genome amplifications, within other output files. Its main use in our lab (https://biocomputationlab.com) is to identify the location and gene locus of transposon inserts in microbial bacterial genomes of Pseudomonas putida KT2440. However, this script can be used for other bacterial genomes for which its genome sequence and annotation are available. Script was developed and tested in python 3.9.5 with blastn version 2.9.0, sickle version 1.33 and fastqc version 0.11.9 This is a description of the LAP entry LAPu-InsertsGenAnnotation-1.0.0 located in the LAP repository
Title: Bacterial genome annotation script using BLASTN v2
Description:
This protocol uses a python based script and command-line BLASTn to annotate in a final table single-read sequencing results from genome amplifications, within other output files.
Its main use in our lab (https://biocomputationlab.
com) is to identify the location and gene locus of transposon inserts in microbial bacterial genomes of Pseudomonas putida KT2440.
However, this script can be used for other bacterial genomes for which its genome sequence and annotation are available.
Script was developed and tested in python 3.
9.
5 with blastn version 2.
9.
0, sickle version 1.
33 and fastqc version 0.
11.
9 This is a description of the LAP entry LAPu-InsertsGenAnnotation-1.
0 located in the LAP repository.
Related Results
Optimizing assembly processes with augmented reality: a case study on TurtleBots
Optimizing assembly processes with augmented reality: a case study on TurtleBots
Augmented reality (AR) technology is revolutionizing traditional assembly processes, offering intuitive and interactive guidance that significantly enhances operational efficiency ...
Principes et outils pour l’annotation des corpus
Principes et outils pour l’annotation des corpus
La linguistique de corpus, c’est à dire les recherches sur le langage portant sur un matériel linguistique écrit ou oral recueilli et conservé, s’est considérablement développée au...
Bacterial genome annotation script using BLASTN v2
Bacterial genome annotation script using BLASTN v2
This protocol uses the command line tools provided by the Python package TnAtlas to identify and annotate transposon integration events in genomes. Given a set of sequencing reads...
Bacterial genome annotation script using BLASTN v2
Bacterial genome annotation script using BLASTN v2
This protocol uses a python based script and command-line BLASTn to annotate in a final table single-read sequencing results from genome amplifications, within other output files. ...
Isolation And Characterization Of Biosurfactant Producing Bacteria From Different Environmental Soil Samples
Isolation And Characterization Of Biosurfactant Producing Bacteria From Different Environmental Soil Samples
Biosurfactants are natural substances produced by several bacterial and fungal organisms that are amphiphilic and are extracellular (a part of the cell membrane). Biosurfactants ca...
Bacterial genome annotation script using BLASTN v1
Bacterial genome annotation script using BLASTN v1
This protocol uses a python based script and command-line blastn to annotate Sanger sequencing results from genome amplifications. Its main use in our lab (https://biocomputationla...
An extensible genome annotation workbench based on the Galaxy Platform
An extensible genome annotation workbench based on the Galaxy Platform
Introduction
Falling costs of genetic sequencing have allowed sequencing and annotation of the genomes of non-model organism. In annotating non-mod...
GAD: a Python script for dividing genome annotation files into feature-based files
GAD: a Python script for dividing genome annotation files into feature-based files
Abstract
Nowadays, manipulating and analyzing publicly available genomic datasets become a daily task in bioinformatics and genomics laboratories...