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iPSORT specifications

Information


Unique identifier OMICS_29156
Name iPSORT
Alternative name caml-iPSORT
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Hideo Bannai <>

Additional information


http://ipsort.hgc.jp/how.html

Information


Unique identifier OMICS_29156
Name iPSORT
Alternative name caml-iPSORT
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages OCaml
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Hideo Bannai <>

Additional information


http://ipsort.hgc.jp/how.html

Publication for iPSORT

iPSORT in pipelines

 (6)
2015
PMCID: 4546252
PMID: 26296655
DOI: 10.1186/s12864-015-1836-2

[…] and subjected to blastx analysis, and 780 ests were identified as ests of fungal origin. the remaining ests either were of plant origin (~53 %) or unknown (~4 %). the orf finder, and signalp and ipsort algorithms were employed to identify open reading frames (orfs) containing putative signal peptide (sp) sequences. twenty-two orfs were predicted to encode proteins with a putative n-terminal […]

2011
PMCID: 3149586
PMID: 21699715
DOI: 10.1186/1471-2164-12-327

[…] sequences (1934 ests) were analyzed for features indicative of secreted proteins. because of directional cloning, we could analyze the coding sequences from the 5'-end. orf finder, and signalp and ipsort algorithms were exploited to deduce orfs and sps within the orfs. one hundred sixty-two predicted orfs (8.37% of the total fungal ests) were predicted to encode proteins with n-terminal sps. […]

2011
PMCID: 3354322
PMID: 22113351
DOI: 10.1007/s00203-011-0773-y

[…] revealed that both exhibit 35% identity (supplements, figure s1). a signal peptide, a propeptide and the n-terminus of the putative mature protein of anisin1 were identified (kyte and doolittle ; ipsort, http://ipsort.hgc.jp/), indicating that anisin1 is an extracellular protein. the mature proteins anisin1 and aadefa1 contain 41 and 40 aa, respectively, and exhibit 51% aa identity (fig. ). […]

2010
PMCID: 2873472
PMID: 20385027
DOI: 10.1186/1471-2164-11-237

[…] pattern for all but schistosoma tgrs; in these latter instances the non-canonical pattern revealed the secis element. topology prediction of the polypeptides was carried out using signalp 3.0 [] and ipsort []. phylogenetic analyses of flatworm and mammalian grs, trs and tgrs were performed on amino acid sequences aligned with clustalw2 []. neighbor-joining, maximum parsimony, minimum evolution […]


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iPSORT in publications

 (119)
PMCID: 5951830
PMID: 29760464
DOI: 10.1038/s41467-018-04250-4

[…] the subcellular localization of c-terminally flag-tagged osgepl1 transiently expressed in hela cells. as shown in fig. , osgepl1 was predominantly localized in mitochondria. consistent with this, ipsort analysis predicted the existence of an mts in the n-terminal region (positions 1–33) of osgepl1 (supplementary fig. ). the osgepl1 variant with the mts truncation (δ2–33) did not translocate […]

PMCID: 5874029
PMID: 29590215
DOI: 10.1371/journal.pone.0194487

[…] proteins (e.g., homologs of bacteria)., the presence of mitochondria-targeting signals in the proteins in question were evaluated using three different programs—mitofates, tppred2 and targetp and ipsort [–]. the n-termini of the predicted proteins were manually curated using the genome and transcriptome data. if n-termini of the proteins predicted from genome data were truncated, […]

PMCID: 5814437
PMID: 29449573
DOI: 10.1038/s41598-018-21340-x

[…] (10%), which apparently lost targeting ability. the reasons for these observations are discussed below.figure 2, potential targeting signal peptides in the b1 protein were identified by running the ipsort and targetp 1.1 programs (fig. ) for the r and k residues. the predicted targeting domains were labeled domain a (32prrar36), domain b (46arrsrr51), domain c (63vrdkrprr70) and domain d […]

PMCID: 5803263
PMID: 29416051
DOI: 10.1038/s41598-018-20687-5

[…] conserved domain search program (http://www.ncbi.nlm.nih.gov/structure/cdd/wrpsb.cgi), and cds-encoding protein characteristics were predicted using the protparam (http://web.expasy.org/protparam/), ipsort (http://ipsort.hgc.jp/), and psipred (http://bioinf.cs.ucl.ac.uk/psipred/) programs., three-month-old wt k. daigremontiana plants were divided into five groups. all groups were treated using […]

PMCID: 5762910
PMID: 29321580
DOI: 10.1038/s41598-017-18760-6

[…] using gsds (http://gsds.cbi.pku.edu.cn/)., protein properties were determined using the online tool protparam (http://web.expasy.org/protparam/) and subcellular localization was predicted using ipsort (http://ipsort.hgc.jp/). conserved motifs were analyzed using the meme suite (http://meme-suite.org/tools/meme) as described before., global gene expression profiles over various tissues […]


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iPSORT institution(s)
Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan; Department of Mathematical Sciences, Tokai University, Kanagawa, Japan; Faculty of Mathematics, Kyushu University, Kyushu University, Fukuoka, Japan

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