RDP FrameBot protocols

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RDP FrameBot specifications

Information


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

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Versioning


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Documentation


Maintainer


  • person_outline James M. Tiedje <>

Additional information


https://github.com/strejcem/FBdenovo

Information


Unique identifier OMICS_01527
Name RDP FrameBot
Alternative names Framebot, FBdenovo
Interface Web user interface
Restrictions to use None
Input data Nucleotide sequence file or protein target sequence file.
Input format FASTA
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.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline James M. Tiedje <>

Additional information


https://github.com/strejcem/FBdenovo

Publications for RDP FrameBot

RDP FrameBot in pipelines

 (4)
2018
PMCID: 5936773
PMID: 29760683
DOI: 10.3389/fmicb.2018.00703

[…] for rapid, accurate and biologically meaningful classification of functional gene sequences in general and nifh in particular, including nearest neighbor identification in pairwise alignment using framebot (), lowest common ancestor parsing of blast bit scores using megan (; ), or cart (). here, we used a combined approach in our pipeline and describe the taxonomic affiliation of the sequences […]

2017
PMCID: 5694480
PMID: 29184545
DOI: 10.3389/fmicb.2017.02226

[…] or 450 nt for aob amoa) were analyzed further. the chimeras of the unique sequences were identified and removed using the uchime algorithm in mothur. the processed sequences were submitted to the framebot () to correct sequencing errors resulting in frameshift. the sequences were clustered into operational taxonomic units (otus) with a cut-off value of 0.07 for aoa amoa and 0.05 for aob amoa […]

2016
PMCID: 4928058
PMID: 27356769
DOI: 10.1038/srep28981

[…] initial process of rdp pipeline to remove low quality (q score <20) and short reads (<300 bp). chimera reads were removed through uchime running in de novo mode. sequences were filtered using framebot to remove non-amoa sequences. sequences were clustered based on cd-hit using operational taxonomic units (otu) pick up program in qiime with nucleotide sequence dissimilarity at 20%. […]

2013
PMCID: 3750361
PMID: 23986751
DOI: 10.3389/fmicb.2013.00243

[…] of the ncbi database. the sequences that did not match the target gene were excluded from further analysis. the remaining sequences were translated by the rdp's functional gene and repository framebot tool (http://fungene.cme.msu.edu/fungenepipeline/framebot/form.spr), which detects and corrects the likely frameshift errors. after removing amino acid sequences with stop codons and/or […]


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RDP FrameBot in publications

 (29)
PMCID: 5936773
PMID: 29760683
DOI: 10.3389/fmicb.2018.00703

[…] to otu centroids using the -usearch_global command (at a 0.97% identity, hereafter referred to as otu97). (4) translation into amino acids and (potential) frameshift corrections were done using framebot () against the nifh protein reference set. (5) homologous genes to the nifh gene (bchx, chll, bchl, and para) were filtered out against the hmm nifh_chll_bchx.hmm (see above) using […]

PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] removed sequences containing incorrect stop codons due to sequencing or pcr errors (e.g., frameshifts) in the region of interest. sequences containing frameshifts were further filtered out using framebot. to facilitate sequence alignment analyses, the dataset was transiently de-replicated using mothur v1.33. selected sequences were aligned based on translated protein sequences with mafft v7 […]

PMCID: 5911990
PMID: 29285891
DOI: 10.1002/mbo3.556

[…] et al., ). then, the chimeric sequences were removed using uchime (edgar, haas, clemente, quince, & knight, ). to accurately detect and correct frameshifts caused by indel sequencing errors, the framebot (wang et al., ) tool was used. briefly, only the sequences containing no ambiguous bases (n), without any barcode or primer mismatches, and with the corrected frameshifts and length (about […]

PMCID: 5705078
PMID: 29182670
DOI: 10.1371/journal.pone.0188223

[…] pipeline []. reads shorter than 400 bp were discarded and chimeras were checked and removed with uchime []. sequences were translated to amino acids and compared to the pmoa reference sequence with framebot for detecting frameshift errors and sequences with inframe stop codons, which were removed. remaining high quality sequences were aligned with hmmer3 and then clustered at 93% similarity, […]

PMCID: 5694480
PMID: 29184545
DOI: 10.3389/fmicb.2017.02226

[…] or 450 nt for aob amoa) were analyzed further. the chimeras of the unique sequences were identified and removed using the uchime algorithm in mothur. the processed sequences were submitted to the framebot () to correct sequencing errors resulting in frameshift. the sequences were clustered into operational taxonomic units (otus) with a cut-off value of 0.07 for aoa amoa and 0.05 for aob amoa […]


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RDP FrameBot 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
RDP FrameBot 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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