ATGpr protocols

View ATGpr computational protocol

ATGpr statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Translation initiation site prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

ATGpr specifications

Information


Unique identifier OMICS_09989
Name ATGpr
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for ATGpr

ATGpr in pipelines

 (4)
2017
PMCID: 5450112
PMID: 28558830
DOI: 10.1186/s13058-017-0853-2

[…] in poly(a)- enriched rna fractions (additional file : figure s2)., based on a blastx analysis of all possible reading frames identified by the open reading frame (orf) finder from the ncbi and atgpr (http://atgpr.dbcls.jp/), lincin lacks the potential to encode any recognizable protein domains. as described previously [], we further examined the coding potential of lincin using […]

2015
PMCID: 4416395
PMID: 25887897
DOI: 10.1186/s12862-015-0326-0

[…] apx sequences appear to be cytosolic. overall protein length varied considerably between cytosolic isoforms (308–453 aa), and multiple start codons could be found within the same orf. nevertheless, atgpr software’s prediction of the “true” start codon in symapx1 was supported by the location of the spliced leader, found 58 bp upstream of the coding sequence in the symapx1 isoform […]

2015
PMCID: 4416395
PMID: 25887897
DOI: 10.1186/s12862-015-0326-0

[…] available est libraries for symbiodinium types a1, b1, c3, d, and f1 in order to obtain additional sequences (table )., sequences were analysed for the presence of open reading frames (orf) using atgpr software [] and translated accordingly. amino acid sequences were analysed using phobius [] for the presence of signal peptides and transmembrane domains, targetp 1.1 [] for prediction […]

2012
PMCID: 3549756
PMID: 23273344
DOI: 10.1186/1471-2148-12-256

[…] their identity determined by blastn similarity searches against the ncbi non-redundant database. nucleotide sequences were analysed for a kozak consensus sequence to identify the start codon using atgpr (atgpr.dbcls.jp) and the corresponding protein sequences were obtained using translate (web.expasy.org/translate). nucleotide data were submitted to genbank under the accession numbers shown […]


To access a full list of citations, you will need to upgrade to our premium service.

ATGpr in publications

 (19)
PMCID: 5822637
PMID: 29466962
DOI: 10.1186/s12885-018-4129-8

[…] translation prediction for the mycnos-01 transcript sequence was carried out using the expasy translate tool (http://web.expasy.org/translate/) [] and kozak sequence prediction was carried out using atgpr (http://atgpr.dbcls.jp/) []., human arms cell line rms-01 was available directly from the authors [] and the rh30 cell line was a gift from peter houghton (st jude children’s research hospital, […]

PMCID: 5762901
PMID: 29321583
DOI: 10.1038/s41598-017-18649-4

[…] exon 1 (fig. ). we analyzed the cdna sequences for the presence of open reading frames (orfs) through coding potential calculator, ncbi’s orffinder, and a translation initiation prediction program (atgpr) but the outcome underscored the non-coding nature of all sox2otb and sox2otc splice variants (supplementary fig. ). to test whether the transcripts can be translated into a polypeptide […]

PMCID: 5648507
PMID: 29047338
DOI: 10.1186/s12861-017-0156-y

[…] truncated protein would lack the first two amino acids of the runt-domain. in addition, the sequence around aug (+73) was predicted to be closer to kozak sequences than aug (+151) according to the atgpr program []. we therefore propose that the position of the non-canonical downstream aug is at +73. interestingly, we found that the amount of truncated p2-runx1 isoform in runx1 δp1:p2taa/ […]

PMCID: 5309803
PMID: 28176794
DOI: 10.1038/ncomms14279

[…] escape nmd and a shorter in-frame pih1d3 protein could be expressed. such an alternative atg indeed exists in exon 4 (codon 61) and it contains a good kozak consensus sequence as predicted by atgpr (score of 0.15 versus 0.16 for the usual atg initiation codon)., we investigated pih1d3-mutated cilia motility using high-speed video microscopy imaging. all affected individuals had immotile […]

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

[…] 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 exist which can provide a splice donor site. until now, we were not able […]


To access a full list of publications, you will need to upgrade to our premium service.

ATGpr institution(s)
Helix Research Institute, Kisarazu-shi, Chiba-ken, Japan

ATGpr reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ATGpr