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FramePlot specifications

Information


Unique identifier OMICS_29536
Name FramePlot
Interface Web user interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA
Programming languages Perl
Computer skills Basic
Version 2.3.2
Stability Stable
Source code URL http://www0.nih.go.jp/~jun/research/frameplot/frameplot-2.3.pl
Maintained Yes

Maintainer


  • person_outline Jun Ishikawa

Publication for FramePlot

FramePlot citations

 (5)
library_books

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic

2017
Sci Rep
PMCID: 5238381
PMID: 28091525
DOI: 10.1038/srep40248

[…] ive genomes or all complete genomes, as well as by performing classic BlastN using the non-redundant nucleotide database nt (identity percentage > 97%).Coding DNA sequences (CDS) were predicted using FramePlot and PROKKA packages. Most of CDS were identical except that PROKKA did not detect the two incomplete CDS at the 5’ extremity of the IL_C4 and IL_B3 clones. The sequences were manually correc […]

library_books

Characterization of a SAM dependent fluorinase from a latent biosynthetic pathway for fluoroacetate and 4 fluorothreonine formation in Nocardia brasiliensis

2014
F1000Res
PMCID: 3999930
PMID: 24795808
DOI: 10.12688/f1000research.3-61.v1

[…] moFisher Scientific Inc.). NMR data were collected using a Bruker 400 MHz spectrometer. Sequence analysis. The genetic open reading frame sequences (ORFs) in N. brasiliensis were identified using the FramePlot 4.0 beta program ( http://nocardia.nih.go.jp/fp4/). The corresponding proteins were compared with other known proteins in the NCBI databases by using available BLAST methods ( http://www.ncb […]

call_split

FK506 biosynthesis is regulated by two positive regulatory elements in Streptomyces tsukubaensis

2012
BMC Microbiol
PMCID: 3551636
PMID: 23083511
DOI: 10.1186/1471-2180-12-238
call_split See protocol

[…] to the GenBank database with accession numbers [JX081655] and [JQ945188], respectively. Web-based versions of sequence database tools (BLAST programs at the NCBI server) and GC-content visualization (FramePlot program) were used for bioinformatic analyses [-]. ClustalW algorithm was used for DNA and protein sequence alignment []. […]

library_books

Genome Sequence of Kitasatospora setae NBRC 14216T: An Evolutionary Snapshot of the Family Streptomycetaceae

2010
PMCID: 2993542
PMID: 21059706
DOI: 10.1093/dnares/dsq026

[…] The prediction of open reading frames (ORFs) was performed using Glimmer3. The initial set of ORFs was manually selected from the prediction result in combination with BLASTP and FramePlot results. Each ORF was annotated manually using in-house genome annotation system OCSS (unpublished). Similarity search results against Uniprot, Interpro and HAMAP databases were used for fun […]

call_split

Architecture of Burkholderia cepacia complex σ70 gene family: evidence of alternative primary and clade specific factors, and genomic instability

2007
BMC Genomics
PMCID: 2194791
PMID: 17784948
DOI: 10.1186/1471-2164-8-308
call_split See protocol

[…] , AlgU (#AAC43714), CnrH (#AAA21967), HrpL (#AAD00805), PpuI (#CAA54870), and RfaY (#AAA92044). All loci encoding putative proteins showing good similarities with the target proteins were analysed by FramePlot [], ORF finder [] and testcode []. BLASTP analyses of the deduced ORF proteins were performed []. Conserved domains among sigma factors were detected using CDD 2.02 []. To achieve saturation […]

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FramePlot institution(s)
Department of Bioactive Molecules, National Institute of Infectious Diseases, Tokyo, Japan

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