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TSSPlant specifications

Information


Unique identifier OMICS_14906
Name TSSPlant
Alternative name TSSP
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A single or multiple query sequences.
Input format FASTA
Output data The final set of predicted transcription start sites (TSSs) for both TATA and/or TATA-less promoter classes.
Output format TXT
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Requirements
GFORTRAN
Maintained No

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Additional information


http://linux1.softberry.com/berry.phtml?topic=tssp&group=programs&subgroup=promoter

Publication for TSSPlant

TSSPlant citations

 (4)
call_split

Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast

2018
BMC Genomics
PMCID: 5838962
PMID: 29510672
DOI: 10.1186/s12864-018-4563-7
call_split See protocol

[…] Transcriptional start sites (TSS) were predicted using TSSPlant []. Experimental verification of TSS was performed with SMARTer™ RACE cDNA Amplification Kit (Clontech) using total RNA from yeast and maize (B73) respectively, which were isolated as describ […]

call_split

The unique evolutionary pattern of the Hydroxyproline rich glycoproteins superfamily in Chinese white pear (Pyrus bretschneideri)

2018
BMC Plant Biol
PMCID: 5816549
PMID: 29454308
DOI: 10.1186/s12870-018-1252-2
call_split See protocol

[…] To identify the potential transcription factor in the promoter sequences of HRGPs, TSSPlant in Softberry Website (http://www.softberry.com/) was used for this analysis []. We extracted the 1000 bp upstream sequences of HRGPs from WGD events and screened against the TSSPlant database […]

library_books

Xylem specific activation of 5’ upstream regulatory region of two NAC transcription factors (MusaVND6 and MusaVND7) in banana is regulated by SNBE like sites

2018
PLoS One
PMCID: 5811034
PMID: 29438404
DOI: 10.1371/journal.pone.0192852

[…] es were designated as PMusaVND7(1237 bp) and PMusaVND6(1143 bp) and were deposited in the NCBI database. Putative TATA box and transcription start site (+1 TSS) was determined by insilico analysis at TSSplant server (http://www.softberry.com/berry.phtml?topic=tssplant&group=programs&subgroup=promoter)Sequence analysis of either PMusaVND7 or PMusaVND6 revealed presence of at least two 19bp perfect […]

library_books

Identification of protein secretion systems in bacterial genomes

2016
Sci Rep
PMCID: 4793230
PMID: 26979785
DOI: 10.1038/srep23080

[…] s sub-type lacked homologs of the “trans-envelope subcomplex” and included nine homologs of the 13 described core components of T6SSi (). Furthermore, it had three specific components (TssN, TssO and TssP) that are absent in the other sub-types of T6SS. Only three loci were reported for this sub-type. We used them to build 13 protein profiles, including the 12 abovementioned proteins and EvpJ. We […]

Citations

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TSSPlant institution(s)
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; Institue of Molecular Biology and Biotechnologies, ANAS, Baku, Azerbaijan; Softberry Inc, Mount Kisco, NY, USA
TSSPlant funding source(s)
This work was supported by the Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) (URF/1/1976-02, FCS/1/2448-01), by the Science Development Foundation under the President of the Republic of Azerbaijan (Grant EIF-2010-1(1)-40/27-3).

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