xFITOM protocols

View xFITOM computational protocol

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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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Maintainer


  • person_outline Ivan Erill <>

Publication for xFITOM

xFITOM in pipeline

2012
PMCID: 3323433
PMID: 22305460
DOI: 10.1186/1471-2164-13-58

[…] γ/β- and the α-proteobacteria were derived from experimental data from e. coli and several α-proteobacteria species as described previously [,]., 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 […]


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xFITOM in publications

 (2)
PMCID: 3422134
PMID: 23032607
DOI: 10.4137/EBO.S9205

[…] considered putative binding sites and added to an expanded collection used as the standard in subsequent genomic searches., 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 […]

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

[…] previously in independent studies as leading to integrase inactivation [,]., 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 […]


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

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