STRING pipeline

STRING specifications

Information


Unique identifier OMICS_11579
Name STRING
Alternative name Search for Tandem Repeats IN Genomes
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Valerio Parisi <>

Publication for Search for Tandem Repeats IN Genomes

STRING citations

 (20)
2018
PMCID: 5892904

[…] kilobase of transcript per million fragments mapped (fpkm). blast2go software was used for gene ontology analysis. gene regulatory network and pathway analysis were done using strink database (www.string-db.org)., rna-seq gene expression profiles for five selected genes were validated by rt-qpcr. ubiquitin-conjugating enzyme and cullin were selected as internal reference genes from the non-de […]

2018
PMCID: 5938574

[…] cell states. in such cases, sequence features that are predictive of tf binding in one cell state may be detrimental to predicting binding in another., singh et al. [218] developed transfer string kernels for svms for cross-context tf binding. domain adaptation methods that allow training neural networks which are transferable between differing training and test set distributions […]

2017
PMCID: 5359670

[…] performed amino acid sequence analysis of htrir by clustal w39 and found that the n terminal of htrir is heterologous while the c-terminal is highly conserved (fig. 2b)., we next did text mining by string22 (http://www.string-db.org/) (fig. 2c) to search other proteins interacting with htrir in addition to the reported snrpa, rpl36, ubc and sf3a2. ddx46, efcab7 and c14orf119 were predicted […]

2017
PMCID: 5370158

[…] current version of the cancer gene census was downloaded 7/22/16, and this version had last been updated by cosmic on 3/26/2016. protein-protein interactions were downloaded from the homo sapiens string v.10.0 network [16] using the aggregate score of all evidence types and were considered as interactions if they had ‘medium confidence’ or higher (interaction score ≥ 0.4). population germline […]

2017
PMCID: 5591210

[…] nucleotide occurs when two specific nucleotides are given. in particular, we applied an interpolated markov model25 to generate more efficient features even in shorter genes with a limited number of string patterns. when the frequency of 2nd-order markov chain is less than 40 bps, 1st-order markov chain was used. such features were calculated for each gene. the results of pca were visualized […]

STRING institution(s)
Sez INFM, Univ Roma ‘Tor Vergata’, Roma, Italy; EuroBioPark, Univ Roma ‘Tor Vergata’, Roma, Italy; Dip Metodi e Modelli Matematici, Univ Roma ‘La Sapienza’ Roma, Italy

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