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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 in publications

 (8)
PMCID: 5749712
PMID: 29293521
DOI: 10.1371/journal.pone.0189673

[…] 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) []., prophage induction was accomplished by adding 5 μg ml-1 mitomycin c to exponentially […]

PMCID: 5217627
PMID: 28056763
DOI: 10.1186/s12864-016-3400-0

[…] is still above fcut. record if the inverse complement is also significant with the same distance;for motif pairs that satisfy the criteria above, investigate their distribution in the genome using pattern locator []. , scan the genome and count the number of times that the pairs of motifs a and b (pentamers in the current application) occur at every spacer distance between 5 and 89 […]

PMCID: 5179023
PMID: 28005945
DOI: 10.1371/journal.pone.0168626

[…] directly upstream of the region of the orthologous gene or in the upstream region of the corresponding transcription unit. the comparison of pal and palg among mycoplasmas genomes were performed by pattern locator software []. differently from the tandem repeat strategy, just two classifications could be assigned to the palg or pal elements: 1) conserved–the inverted repeat that composed […]

PMCID: 5001606
PMID: 27307602
DOI: 10.1093/nar/gkw543

[…] bank with id 5d8c (wild-type hinmlr:padhc-estd/nmlr(wt) dna complex); 5e01 (wild-type hinmlr:padhc-estd/nmlr(sym) dna complex); 5d90 (wild-type hinmlr). sequence patterns were identified using the pattern locator server (http://www.cmbl.uga.edu/software/patloc.html) ()., in n. meningitidis and h. influenzae, nmlr controls expression of an operon consisting of two genes, adhc and estd, involved […]

PMCID: 4901048
PMID: 27375608
DOI: 10.3389/fmicb.2016.00904

[…] was highly expressed), such as lysr (xf1721), acts (xf2577), trpr (xf1920), and opde (xf1749) (http://www.lbi.ic.unicamp.br/xf/), as shown by muranaka et al. (), either manually or using the patloc (pattern locator) online software (http://www.cmbl.uga.edu/software/patloc.html) did not reveal any possible regulatory sequences similar to the ones found in x. fastidiosa and e. coli (figure ). […]


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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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