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Pattern locator specifications

Information


Unique identifier OMICS_15388
Name Pattern locator
Interface Web user interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA or GenBank
Output data Locations of the patterns found, the actual nucleotide sequences and their flanks, and overlapping patterns.
Programming languages C, Python
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Source code URL http://www.cmbl.uga.edu/downloads/programs/Pattern_Locator/patloc.c
Maintained Yes

Maintainer


  • person_outline Jan Mrazek

Information


Unique identifier OMICS_15388
Name Pattern locator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA or GenBank
Output data Locations of the patterns found, the actual nucleotide sequences and their flanks, and overlapping patterns.
Operating system Unix/Linux
Programming languages C, Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jan Mrazek

Publication for Pattern locator

Pattern locator citations

 (4)
library_books

Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon like appendages

2018
PLoS One
PMCID: 5749712
PMID: 29293521
DOI: 10.1371/journal.pone.0189673

[…] ein sequences was monitored with Lalign version 36.3.5e [], internal repeat sequences were detected with Internal Repeats Finder [], DUF11 was located with MyHits [] and putative promoters located by Pattern Locator []. Prophage sequences were identified and annotated by PHAST (http://phast.wishartlab.com) []. […]

library_books

Genome evolution in an ancient bacteria ant symbiosis: parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini

2015
PeerJ
PMCID: 4389277
PMID: 25861561
DOI: 10.7717/peerj.881

[…] For B. pennsylvanicus (NC_007292), B. obliquus, and B. turneri, we used DNAPlotter () to construct plots of GC skew with 500 bp window size and 50 bp step size. We used Pattern Locator () to search these three genome sequences for the consensus DnaA box motif TTWTNCACA. […]

call_split

Assessing Diversity of DNA Structure Related Sequence Features in Prokaryotic Genomes

2014
PMCID: 4060949
PMID: 24408877
DOI: 10.1093/dnares/dst057
call_split See protocol

[…] Pattern Locator was used to count loci in each analysed sequence that matched the sequence pattern at hand (the observed count). The expected count of matching loci was determined as the average numbe […]

library_books

Unprecedented loss of ammonia assimilation capability in a urease encoding bacterial mutualist

2010
BMC Genomics
PMCID: 3017870
PMID: 21126349
DOI: 10.1186/1471-2164-11-687

[…] We used the Pattern Locator program [] to search the B. vafer genome for dnaA boxes using the consensus sequence TTWTNCACA []. In the absence of a characteristic cluster of dnaA boxes, we used the CGview Server [ […]

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Pattern locator institution(s)
Department of Microbiology and Institute of Bioinformatics, Athens, GA, USA; Department of Computer Science, University of Georgia, Athens, GA, USA
Pattern locator funding source(s)
This work was supported in part by a Faculty Research Grant from the University of Georgia Research Foundation, Inc.

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