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Detects and corrects frameshift errors caused by insertions and deletions in DNA sequences. RDP FrameBot uses a dynamic programming technique similar to that used for pairwise protein alignment but uses three sets of two-dimensional (2D) matrices, one for each potential reading frame. The software corrects frameshift errors in query reads and determines their closest matching protein sequences in a set of reference sequences.

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RDP FrameBot forum

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RDP FrameBot classification

RDP FrameBot specifications

Unique identifier:
OMICS_01527
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Java
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Alternative names:
Framebot, FBdenovo
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
1.2.0
Source code URL:
https://codeload.github.com/rdpstaff/Framebot/tar.gz/1.2.0

RDP FrameBot distribution

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RDP FrameBot classification

RDP FrameBot specifications

Unique identifier:
OMICS_01527
Interface:
Web user interface
Input data:
Nucleotide sequence file or protein target sequence file.
Output data:
Dereplicated nucleotide file with sample mapping and ids, frameshift corrected protein and nucleotide sequences and frameBot statistics including closest match to reference for each query sequence.
Stability:
Stable
Alternative names:
Framebot, FBdenovo
Restrictions to use:
None
Input format:
FASTA
Computer skills:
Basic
Maintained:
Yes

RDP FrameBot support

Documentation

Maintainer

  • James M. Tiedje <>
  • James M. Tiedje <>

Additional information

https://github.com/strejcem/FBdenovo

Credits

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Publications

Institution(s)

Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA; School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea; Computer Science and Engineering Department, Michigan State University, East Lansing, MI, USA

Funding source(s)

Supported by the Office of Science (BER), U.S. Department of Energy, grant DE-FG02-99ER62848, DE-FG02-07ER64398, and DE-FC02-07ER64494 (DOE Great Lakes Bioenergy Research Center), NIH Human Microbiome Project Demonstration Project (UH3DK083993), and NEON Inc.

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