Main logo
?
tutorial arrow
×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

ImmuneDB

Analyzes vast amounts of IGHV (immunoglobulin heavy-chain variable) sequences and exploring the resulting data. ImmuneDB can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files. After analysis, resulting data can then be easily visualized, queried, and exported through its web-based interface.

User report

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

0 user reviews

No review has been posted.

ImmuneDB forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

ImmuneDB classification

ImmuneDB specifications

Software type:
Framework/Library
Restrictions to use:
None
Output data:
A web interface to ImmuneDB is provided, allowing users to interactively explore data after analysis with the pipeline. Most data including raw sequences, metadata, mutation analysis, and clonal assignments can be easily downloaded in a variety of formats including FASTA, FASTQ, and CSV allowing further processing with external tools.
Programming languages:
Python
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Input data:
ImmuneDB takes as input raw FASTA or FASTQ files with full or partial IGHV sequences, optionally pre-processed by pRESTO.
Operating system:
Unix/Linux
Database management system:
MySQL
Stability:
Stable

ImmuneDB distribution

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

download

ImmuneDB support

Maintainer

  • Uri Hershberg <>

Additional information

A free trial is available on the site.

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

Institution(s)

School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA

Funding source(s)

This work was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Number P01AI106697 and by NIH P30-CA016520.

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.