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SEED2 specifications


Unique identifier OMICS_27009
Name SEED2
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data A protein sequence, etc.
Input format FASTA,FASTQ,TXT
Biological technology Illumina
Operating system Windows
Computer skills Medium
Stability Stable
Registration required Yes
Maintained No


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Publication for SEED2

SEED2 citations


Knockdown of MALAT1 expression inhibits HUVEC proliferation by upregulation of miR 320a and downregulation of FOXM1 expression

PMCID: 5617440
PMID: 28977880
DOI: 10.18632/oncotarget.18507

[…] by DNA sequencing before use.For the dual luciferase reporter assay, HEK293T cells were co-transfected with 150 ng of a firefly luciferase reporter plasmid pGL3-MALAT1-Seed1 (Seed1), or pGL3- MALAT1-Seed2 (Seed2) and a renilla luciferase vector (pRL-SV40, Promega) plus small RNAs (miR-101 mimics or negative control RNAs) using Lipofectamine 2000 (Invitrogen). pGL3-FOXM1-UTR-wt and pGL3-FOXM1-UTR- […]


Erroneous energy generating cycles in published genome scale metabolic networks: Identification and removal

PLoS Comput Biol
PMCID: 5413070
PMID: 28419089
DOI: 10.1371/journal.pcbi.1005494

[…] One of the simplest EGCs we identified is displayed in . This cycle is contained in only two metabolic models from The ModelSEED database, Klebsiella pneumoniae MGH 78578 (Seed272620.3) and Flavobacterium johnsonia johnsoniae UW101 (Seed376686.6). In this EGC, a malate symporter (rxn10153) transports malate together with two protons out of the cell. The exported malate […]


MiR 199a 3p suppresses proliferation and invasion of prostate cancer cells by targeting Smad1

PMCID: 5581043
PMID: 28881744
DOI: 10.18632/oncotarget.17191

[…] Smad1 3′ UTR had two binding sites of miR-199a-3p (Seed1: 5′-ACCTCTGTGACCAAC TATTG-3′; Seed2: 5′-AACTGTATGCTGGCTGTATTACTGT-3′). We constructed mutant Smad1 3′ UTR by site-directed mutagenesis kit (Stratagene, USA) (Seed1 mut: 5′-ACCTCTGTGACCATAATTTG-3′; Seed2 mut: 5′-AACTGTATGCTGGCTGTAT […]


Homology Aware Phylogenomics at Gigabase Scales

Syst Biol
PMCID: 5790135
PMID: 28123115
DOI: 10.1093/sysbio/syw104

[…] ing -mer blocks into data sets of blocks each, where was 25, 100, or 1000. Bootstrap majority rule ML trees for the 1426 data sets for set were constructed using RAxML (raxmlHPC-AVX -m GTRGAMMA -x seed2 -# 100 -s alignmentFile -n outfilesname -p seed1). Each of these data sets comprised bp alignments. The discordance pattern among these gene trees was quantified and visualized as a consensus n […]


Monte Carlo calculations and experimental measurements of the TG‐43U1‐recommended dosimetric parameters of 125I (Model IR‐Seed2) brachytherapy source

PMCID: 5690036
PMID: 27455485
DOI: 10.1120/jacmp.v17i4.6127

[…] Characteristics of the Model IR‐Seed2 source were determined according to the recommendations of the Task Group 43 (TG‐43U1) by the American Association of Physicists in Medicine (AAPM)., Following this protocol, the spatial dose r […]


Genome Wide Identification, Evolutionary Analysis, and Stress Responses of the GRAS Gene Family in Castor Beans

Int J Mol Sci
PMCID: 4964380
PMID: 27347937
DOI: 10.3390/ijms17071004

[…] global expression profiles of GRAS genes identified in castor beans were analyzed based on our previous Tag-seq data []. In brief, all clean reads from leaf, root, seed1 (15 days after pollination), seed2 (35 days after pollination), and endosperm tissues (40 days after pollination) described earlier were mapped to the castor bean genome ( using SOAP2 software […]


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SEED2 institution(s)
Institute of Microbiology of the CAS, Prague, Czech Republic
SEED2 funding source(s)
Supported by the Ministry of Education, Youth and Sports of the Czech Republic [LM2015055].

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