PatScan protocols

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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


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


Add your version

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 in pipelines

 (6)
2017
PMCID: 5399378
PMID: 28427349
DOI: 10.1186/s12864-017-3707-5

[…] 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 […]

2012
PMCID: 3463484
PMID: 22978558
DOI: 10.1186/1471-2164-13-481

[…] were then sorted by sequence identity, the size variants identified, and the relative count of each mirna was determined. unique srna sequences were queried against known mirnas using the program patscan [] with default parameters and two mismatches in order to identify homologs of known mirnas. flanking sequences (150 nt at each side) of the mature mirna were retrieved and folded using […]

2012
PMCID: 3505464
PMID: 22721355
DOI: 10.1186/1471-2164-13-264

[…] with annotated rice mirnas and their precursors in mirbase (version 16.0, http://www.mirbase.org); homologs of the indica 93–11 genome were regarded as mature mirnas and mirna precursors based on patscan searches (mismatch < =2, insertion = 0, deletion = 0). mirnas located at the position ±2 nt of the precursors were also included as mature mirnas. new mirna prediction was based […]

2010
PMCID: 3017389
PMID: 21147880
DOI: 10.1093/gbe/evq082

[…] transfer rnas (trnas) were identified with trnascan-se (; http://lowelab.ucsc.edu/trnascan-se/). rrna genes were identified by blastn. to search for small nuclear rnas (snrnas), a local patscan search was employed with consensus sequences of known snrnas used as a guide (). the c. paramecium nucleomorph genome sequence has been deposited in genbank under accession number cp002172 […]

2009
PMCID: 2714311
PMID: 19534778
DOI: 10.1186/1471-2202-10-60

[…] human amino acid sequences of the family as the queries. for phylogenic analysis, mrna sequences were translated into amino acid sequences. the analyses for conserved motifs were performed by the scan for matches [], weeder [] and jasper []. multiple alignment of pmp22 was performed by lagan [] and presented by vista []., pmp22: peripheral myelin protein 22; cmt1a: charcot-marie-tooth disease […]


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PatScan in publications

 (60)
PMCID: 5485520
PMID: 28587281
DOI: 10.3390/genes8060156

[…] (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 […]

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

[…] two parallel arms of the hairpin structure, and are not exactly complementary in sequence (see fig. ). so we tentatively predict the positions of 5p and 3p mirnas by detecting paired segments using patscan although we do not know which of 5p and/or 3p is the actual mirna [, , ]. for those precursors, in which patscan failed to find the paired sequences, a modified li’s method was used to find […]

PMCID: 5363317
PMID: 28345006
DOI: 10.1016/j.omtm.2017.01.005

[…] of on- or off-target activity. low-frequency off-target sites can manifest as single integration sites rather than cliss. to validate true off-target sites, we used the sequence pattern match tool “scan-for-matches.” for this, regions upstream and downstream of all integration sites were scanned for potential binding sites with a maximum distance of 10 bp between integration site and predicted […]

PMCID: 5159562
PMID: 27789695
DOI: 10.1093/nar/gkw987

[…] spectra accumulations. after a baseline correction, spectra were expressed in terms of differential optical density., the human reference genome sequence (build hg19) was scanned using the program patscan () for all 17 nucleotide motifs consistent with the sequence requirements of gtp-binding or peroxidase activity using the models shown in figure . both strands were included in the search, […]

PMCID: 4989117
PMID: 27413050
DOI: 10.1093/molbev/msw122

[…] this motif were used to train a first “lokisecis” infernal model (), using rnaalifold () to predict a consensus rna structure and emacs ralee () to inspect it. a pattern expression for the program scan_for_matches (http://blog.theseed.org/servers/2010/07/scan-for-matches.html, last accessed june 22, 2016) was also manually designed to fit the occurrences of this motif in loki selenoproteins. […]


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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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