PatScan statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PatScan
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Tool usage distribution map

This map represents all the scientific publications referring to PatScan per scientific context
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Associated diseases

This word cloud represents PatScan usage per disease context
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Protocols

PatScan specifications

Information


Unique identifier OMICS_29651
Name PatScan
Alternative names scan_for_matches, PatScanUI
Interface Web user interface
Restrictions to use None
Input data A DNA or a protein sequence.
Input format FASTA
Output format FASTA,GFF3,BED
Programming languages Javascript, Python
License GNU Affero General Public License version 3
Computer skills Basic
Stability Stable
Maintained Yes

Download


github.png

Documentation


Maintainers


  • person_outline Tilmann Weber
  • person_outline Kai Blin

Additional information


Information related to the command-line version can be found at http://blog.theseed.org/servers/2010/07/scan-for-matches.html

Information


Unique identifier OMICS_29651
Name PatScan
Alternative names scan_for_matches, PatScanUI
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A pattern of interest and a set of sequence to scan.
Output format FASTA
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Source code URL http://www.theseed.org/servers/downloads/scan_for_matches.tgz
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Tilmann Weber
  • person_outline Kai Blin

Additional information


Information related to the command-line version can be found at http://blog.theseed.org/servers/2010/07/scan-for-matches.html

Publications for PatScan

PatScan citations

 (42)
library_books

Genome Wide Identification and Characterization of Salinity Stress Responsive miRNAs in Wild Emmer Wheat (Triticum turgidum ssp. dicoccoides)

2017
Genes
PMCID: 5485520
PMID: 28587281
DOI: 10.3390/genes8060156

[…] RNA (snoRNA), etc.) annotation, and the annotated reads were removed. The remaining small RNA reads were used for BLAST against all of the mature plant miRNAs deposited in miRbase release 21 [] using Patscan [] to identify conserved miRNAs. The criteria to define potential conserved miRNAs is no more than 2 mismatches. For the novel miRNA identification, to avoid repeated prediction and reduce the […]

library_books

Genome wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi

2017
BMC Genomics
PMCID: 5399378
PMID: 28427349
DOI: 10.1186/s12864-017-3707-5

[…] d genomic regions were retrieved separately and extended for additional 20 bp from both 5′ and 3′ ends. Potential miRNAs with no more than two mismatches with known metazoan miRNAs were identified by patscan [, , ], and the candidates were folded by RNAfold [, ] subsequently. Unmatched sequences were trimmed. If more than one miRNA were mapped to the overlapping position, only the best one with th […]

library_books

Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems

2016
Mol Biol Evol
PMCID: 4989117
PMID: 27413050
DOI: 10.1093/molbev/msw122

[…] e lokiSECIS of the other Loki selenoprotein genes, has also several important differences (see Results and ), which make it evade the detection power of both the enriched lokiSECIS infernal model and patscan pattern. RNAz did not report any significant hits other than those just described. We built an additional infernal model for the SPS lokiSECIS structure, and incorporated it in the program lok […]

call_split

A Functional oriT in the Ptw Plasmid of Burkholderia cenocepacia Can Be Recognized by the R388 Relaxase TrwC

2016
Front Mol Biosci
PMCID: 4853378
PMID: 27200362
DOI: 10.3389/fmolb.2016.00016
call_split See protocol

[…] oys the Maximum Likelihood method based on the JTT matrix-based model (Koichiro et al., ). GenScript bioinformatics software was selected to analyze AT content (http://www.genscript.com). The program Scan for Matches was used to localize IRs having at least 5 bp in length and less than two mismatches (http://www.theseed.org/servers/downloads/scan_for_matches.tgz). Other intergenic regions of the s […]

library_books

Expression Profiling of Preadipocyte MicroRNAs by Deep Sequencing on Chicken Lines Divergently Selected for Abdominal Fatness

2015
PLoS One
PMCID: 4326283
PMID: 25675096
DOI: 10.1371/journal.pone.0117843

[…] were removed.The remaining short reads that could not be matched to known chicken miRNA precursors were searched against the metazoan mature miRNAs in the Sanger miRBase (20.0) [], using the program Patscan to identify conserved miRNAs, with two mismatches allowed.To find new miRNAs, we first removed those short reads sequenced less than twice in both libraries, and the remaining short reads were […]

library_books

Overview of research on Bombyx mori microRNA

2014
PMCID: 4222307
PMID: 25368077
DOI: 10.1093/jis/14.1.133

[…] , and a novel small RNA were identified in B. mori. Among those identified, there were 12 pairs of miRNAs and miRNA*s ( ). In other applications of miRNA predictive bioinformatics, used miRscan and PatScan algorithms and predicted 120 iRNA genes on the 6x and 9x genome assembly of B. mori based on sequence conservation and structural similarity to known miRNAs. […]


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PatScan institution(s)
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark; Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University of Tubingen, Tubingen, Germany
PatScan funding source(s)
Supported by the Novo Nordisk Foundation [NNF10CC1016517, NNF16OC0021746]; and the German Ministry of Education and Research (BMBF) [0315585A].

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