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“Blaster” – a graphical user interface for common sequence analysis tools

“Blaster” – a graphical user interface for common sequence analysis tools - Published in JOSS (2019)

https://github.com/snowformatics/blasterqt

Science Score: 93.0%

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    Found 4 DOI reference(s) in README and JOSS metadata
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    Links to: ncbi.nlm.nih.gov
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Last synced: 6 months ago · JSON representation

Repository

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Basic Info
  • Host: GitHub
  • Owner: snowformatics
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 53.4 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 1
  • Open Issues: 2
  • Releases: 1
Created over 11 years ago · Last pushed almost 5 years ago
Metadata Files
Readme License

README.md

BlasterQtv1.4

Common sequence alignment tools such as Basic Local Alignment Search Tool (BLAST) or Bowtie short sequence aligner are used by scientist on a daily basis. Often those programs are with command line interface which makes them very practical for developers and advance users but hard for researchers who are more familiar with a graphical user interface. Here we present a tool called Blaster, which offers simple and intuitive graphical interface for performing some of the most common tasks in nucleotide and protein sequence work. The software is provided with the following modules:

    Sequence similarity search (blastn, blastp, blastx, tblastn, tblastx, Bowtie) in local databases

    Multiple sequence alignment (CLUSTALW2)

    Sequence extraction from multiple FASTA files by sequence ID

    Sequence converter (reverse complement, reverse, translate)

    Sequence format conversions (FASTA, Multiple FASTA, FASTQ, CSV)

    Local sequence database management

Screenshots

Alt text Alt text Alt text

Installation

We strongly recommend to install "Blaster" with the Microsoft Windows installer which can be downloaded here http://dx.doi.org/10.5447/IPK/2019/23.

For manual installation, the following dependencies are required:

  • Python 2.7 (https://www.python.org/download/releases/2.7/)
  • Biopython (pip install biopython)
  • PyQt4 (https://sourceforge.net/projects/pyqt/)
  • Blast+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.19/)
  • Bowtie (https://sourceforge.net/projects/bowtie-bio/)
  • clustalw2 (http://www.clustal.org/download/current/)

Manual

http://labtools.ipk-gatersleben.de/help/BlasterQt/BlasterQt.pdf

Bug reports and tests

Bug reports can be either sent by Email (lueckATipk-gatersleben.de) or reported as issue on Github (prefered). If possible and not confidential, upload or link the problematic database or sequence files.

For testing the general functionality of the software, follow the instructions in testing_guideline.txt file in folder test. All required testing files can be found in the same folder.

Contributions

All kind of contributions (documentation, testing, adding more features, suggestions...) are highly appreciated.

History

Blaster v. 1.3

  • Removed FASTQ conversation feature
  • Removed editing database names
  • Updated documentation
  • Bug fixes
  • "." or spaces in database names will be replaced with "_" (see https://github.com/snowformatics/BlasterQt/issues/9)

Blaster v. 1.4

  • Updated documentation
  • Bug fixes
  • Added ".fa" extension
  • Updated test material
  • Create DOI for windows installer

Owner

  • Name: snowformatics
  • Login: snowformatics
  • Kind: user

https://www.buymeacoffee.com/snowforamtics

JOSS Publication

“Blaster” – a graphical user interface for common sequence analysis tools
Published
December 18, 2019
DOI
Volume 4, Issue 44, Page 1411
Authors
Stefanie Lueck ORCID
Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung Gatersleben, Stadt Seeland, Sachsen-Anhalt
Dimitar Douchkov ORCID
Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung Gatersleben, Stadt Seeland, Sachsen-Anhalt
Editor
Lorena Pantano ORCID
Tags
sequences fasta clustalw blast bowtie bioinformatic GUI Windows
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