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NetStart specifications

Information


Unique identifier OMICS_09991
Name NetStart
Interface Web user interface
Restrictions to use None
Input data Sequence(s)
Input format FASTA
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Anders Gorm Pedersen <>

Publication for NetStart

NetStart in pipeline

2015
PMCID: 4672141
PMID: 26688806
DOI: 10.1155/2015/695947

[…] russia). the online tool oligocalc [] was used for primer design. alignments of small sequence sets were generated using multalin []. translation initiation site prediction was performed using netstart 1.0 []., sequencing generated 52,021,865 reads from the “nodules” library and 17,684,604 reads from the “root tips” library. after removal of adapter and index sequences, 75.1% reads […]


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NetStart in publications

 (28)
PMCID: 5729406
PMID: 29237418
DOI: 10.1186/s12881-017-0508-2

[…] exon 2 (fig. , a2). computer analysis performed on this small segment of genomic dna (chr4:102,861,131–102,861,212) did not identify the existence of any genes. in both variants, in silico analysis (netstart1, http://www.cbs.dtu.dk) predicted a translational start site in the beginning of exon 2 which resulted in a frame shift, introducing amino acids changes and a premature stop codon (fig. , […]

PMCID: 5290616
PMID: 28152994
DOI: 10.1186/s12859-017-1502-6

[…] and tsvm approaches were implemented in the transdutis tool, transdutis-i and transdutis-t respectively, available in a web interface. these approaches were compared with the tishunter, tis miner, netstart tools, presenting satisfactory results., in relation to precision, the results are similar for the isvm and tsvm classifiers. however, the results show that the application of tsvm approach […]

PMCID: 5279758
PMID: 28135309
DOI: 10.1371/journal.pone.0170694

[…] first possible open reading frame will start in exon three. analysis with translation start site prediction tools [,] indicated that the corresponding atg codon in exon 3 can serve as start codon (netstart 1.0 [] prediction scores for exon 1: 0.890, score for exon 3: 0.518; atgpr [] reliability for exon 1: 0.60, for exon 3: 0.13). alternatively, an additional exon upstream of exon one might […]

PMCID: 5175197
PMID: 28000783
DOI: 10.1038/srep39608

[…] useful tool to investigate the detailed molecular mechanisms of itl ()., our findings support the need for the careful design of genome-editing vectors for complete null mutations. for example, the netstart 1.0 prediction server can be used to search for potential itl initiation codons when designing vectors for genome editing. for gli3, in addition to the native initiation codon at +1, […]

PMCID: 4946873
PMID: 27416025
DOI: 10.1371/journal.ppat.1005685

[…] genes of the plbj-1 and plfj-1 strains were obtained according to the method in []. eugene, version 4.1 [], was used to integrate multiple sources, including transcription start sites identified by netstart [], homologous proteins identified from the swiss-prot database, version 2015-07-22, by blast, version 2.2.26, the assembled transcripts generated by idba-tran, version 1.1.1 [], […]


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NetStart institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

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