RDP FrameBot statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RDP FrameBot
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Tool usage distribution map

This map represents all the scientific publications referring to RDP FrameBot per scientific context
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Associated diseases

This word cloud represents RDP FrameBot usage per disease context
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Protocols

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

Download


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Versioning


No version available

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 citations

 (36)
library_books

Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP – A Bioinformatics Pipeline for Analyzing nifH Amplicon Data

2018
Front Microbiol
PMCID: 5936773
PMID: 29760683
DOI: 10.3389/fmicb.2018.00703

[…] re 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 […]

library_books

Unifying the global phylogeny and environmental distribution of ammonia oxidising archaea based on amoA genes

2018
Nat Commun
PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] also 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 ( […]

library_books

The effect of bio irrigation by the polychaete Lanice conchilega on active denitrifiers: Distribution, diversity and composition of nosZ gene

2018
PLoS One
PMCID: 5800672
PMID: 29408934
DOI: 10.1371/journal.pone.0192391

[…] Fastqc v0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) [].We eliminated potential chimeras using the USEARCH package [,]. Non-target reads (non-nosZ reads) were filtered out using FrameBot included in the Fungene pipeline (http://fungene.cme.msu.edu/). We retrieved a reference set of nosZ protein sequences of 163 different species with high scores (>919) and 98% coverage with a […]

call_split

High‐throughput analysis of anammox bacteria in wetland and dryland soils along the altitudinal gradient in Qinghai–Tibet Plateau

2017
PMCID: 5911990
PMID: 29285891
DOI: 10.1002/mbo3.556
call_split See protocol

[…] raso 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 29 […]

call_split

Colonic Butyrate Producing Communities in Humans: an Overview Using Omics Data

2017
mSystems
PMCID: 5715108
PMID: 29238752
DOI: 10.1128/mSystems.00130-17
call_split See protocol

[…] d, filtered for a length of ≥70% median gene length of respective reference sequences from genomes, and subjected to chimera removal (UCHIME [v. 4.2.40] using HMM seed sequences as references []) and FrameBot analysis (v. 1.2, in default mode, with all dereplicated references obtained from genome screenings []). For subsequent complete-linkage clustering (default mode []), proteins were aligned to […]

library_books

Diversity and potential activity of methanotrophs in high methane emitting permafrost thaw ponds

2017
PLoS One
PMCID: 5705078
PMID: 29182670
DOI: 10.1371/journal.pone.0188223

[…] e 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, whi […]


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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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