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Target-align specifications

Information


Unique identifier OMICS_04005
Name Target-align
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Unique identifier OMICS_04005
Name Target-align
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for Target-align

Target-align in publications

 (8)
PMCID: 5764023
PMID: 29320982
DOI: 10.1186/s12864-017-4425-8

[…] mrna target of mirna, the rice mature mirna sequences deposited in the mirbase database (http://www.mirbase.org/index.shtml) were downloaded, and then the mirna and cdna sequences were uploaded into target-align with default settings (a score cut-off of ≥70 and mismatch ≤4 nucleotides) []., microarray gene expression data were available at the rice expression profile database (ricexpro, […]

PMCID: 4711666
PMID: 26731407
DOI: 10.1371/journal.pone.0146374

[…] []., the 5′ and 3′ untranslated regions of horse genes were extracted from the ensembl horse genome release 78 (http://www.ensembl.org/). a search for mirna target genes was performed using target-align [] with the following parameters [–]: (1) no more than four mismatches between the small rna and its target (g–u nucleotides count as 0.5 mismatches); (2) no more than two adjacent […]

PMCID: 4337329
PMID: 25755657
DOI: 10.3389/fpls.2015.00058

[…] been widely used (rhoades et al., ; jones-rhoades and bartel, ; fahlgren and carrington, ). ready-to-use online tools include rnahybrid (krüger and rehmsmeier, ), uea srna-tools (moxon et al., ), target-align (xie and zhang, ), psrnatarget (dai and zhao, ) and pmted (sun et al., ). all of these use algorithms that rely mostly on sequence complementarity analysis, implementing filtering […]

PMCID: 4294137
PMID: 25642232
DOI: 10.3389/fpls.2014.00761

[…] of pgdd was used to identify syntenic regions (colinear blocks) containing pvnf-y loci using default parameters (lee et al., ). mir169 target sites in nf-ya family members were identified with target-align (xie and zhang, ) using default parameters. the presence of uorf in p. vulgaris nf-ya genes was analyzed using vector nti (invitrogen, www.lifetechnolgies.com), allowing a minimum length […]

PMCID: 3936892
PMID: 24559317
DOI: 10.1186/1471-2164-15-146

[…] prediction is a common approach for predicting mirna target genes. in recent years, many computational tools have been developed for predicting plant mirna targets, such as psrnatarget [], target-align [], tapir [], and pmrd []. 5′-modified race is frequently used to demonstrate mirna targets. this method is easy to operate, and the results are reliable. however, 5′-modified race […]


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Target-align institution(s)
Department of Biology, East Carolina University, Greenville, NC, USA

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