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Protocols

xFITOM specifications

Information


Unique identifier OMICS_22246
Name xFITOM
Interface Graphical user interface
Restrictions to use None
Input data A collection of aligned sites and a collection of target sequences.
Input format FASTA,RTF,GenBank
Output format CSV
Operating system Windows
Programming languages C++
Computer skills Medium
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Ivan Erill

Publication for xFITOM

xFITOM citations

 (4)
library_books

The Verrucomicrobia LexA Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response

2016
Front Mol Biosci
PMCID: 4951493
PMID: 27489856
DOI: 10.3389/fmolb.2016.00033

[…] ylacidiphilum infernorum V4, TaxID: 481448; 2,287,145 bp) were obtained from the NCBI RefSeq database (RefSeq, RRID:SCR_003496). LexA-binding motif searches on individual genomes were performed using xFITOM (xFITOM, SCR_014445) with the sequence information content (Ri) scoring method and default parameters (Schneider, ; Bhargava and Erill, ). Comparative genomics analyses were performed with CGB, […]

library_books

Inference of Self Regulated Transcriptional Networks by Comparative Genomics

2012
Evol Bioinform Online
PMCID: 3422134
PMID: 23032607
DOI: 10.4137/EBO.S9205

[…] In silico searches of putative binding sites were performed with FITOM and xFITOM (http://compbio.umbc.edu/software). These programs take in a collection of known sites, from which they derive a Position-Specific Frequency Matrix (PSFM). Different scoring methods based on in […]

call_split

Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes

2012
BMC Genomics
PMCID: 3323433
PMID: 22305460
DOI: 10.1186/1471-2164-13-58
call_split See protocol

[…] Comparative genomics analyses were carried out using xFITOM, a program for binding site search in genomic sequences [,]. All chromosome sequences were searched for putative LexA-binding sites using the Ri index [] and a motif-normalized threshold as rep […]

library_books

Prevalence of SOS mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons

2011
Mob DNA
PMCID: 3108266
PMID: 21529368
DOI: 10.1186/1759-8753-2-6

[…] The presence of LexA binding sites on all the retrieved intI homolog sequences was assessed by scanning them using xFITOM http://compbio.umbc.edu/2280/, a generic program for binding site search in genomic sequences [,]. Searches were conducted using the Ri index [] and a motif-normalized threshold as reported pre […]

Citations

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xFITOM institution(s)
Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA

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