Signal-3L protocols

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Signal-3L specifications

Information


Unique identifier OMICS_18488
Name Signal-3L
Interface Web user interface
Restrictions to use None
Input data Some protein sequences.
Input format FASTA
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Hong-Bin Shen <>

Publications for Signal-3L

Signal-3L in pipelines

 (2)
2017
PMCID: 5397871
PMID: 28425468
DOI: 10.1038/srep46163

[…] database using blastx (e-value ≤ 1e-5). the coding dna sequence (cds) and deduced amino acid sequence were obtained using open reading frame finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). signal-3l was used to identify signal peptides and predgpi predictor to identify glycosylphosphatidylinositol (gpi) domains. oligonucleotide primers were designed according to thornton and basu […]

2016
PMCID: 4773003
PMID: 26930070
DOI: 10.1371/journal.pone.0150254

[…] replicates. the analysis was conducted with mega 5.01 []., prediction of subcellular localization, signal peptide and transmembrane domains were conducted using default settings of suba 3 [], signal-3l [] and tmhmm [], respectively. expression profiles for mwl-1 and 2, across different developmental stages, was extracted from the bio-analytic resource for plant biology […]


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Signal-3L in publications

 (28)
PMCID: 5436662
PMID: 28545143
DOI: 10.1371/journal.pone.0177199

[…] signal-blast [] analysis indicated that the first 19, 20 and 19 aa of the n-termini of cdta, cdtb and cdtc, respectively are signal peptides. both predsi (http://www.predisi.de/home.html) and signal-3l [] (http://www.csbio.sjtu.edu.cn/bioinf/signal-3l/) analysis indicate that the first n-terminal 19 aa and of cdta and cdtc, and 21 aa of cdtb are signal peptides ()., based on the signal […]

PMCID: 5397871
PMID: 28425468
DOI: 10.1038/srep46163

[…] database using blastx (e-value ≤ 1e-5). the coding dna sequence (cds) and deduced amino acid sequence were obtained using open reading frame finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). signal-3l was used to identify signal peptides and predgpi predictor to identify glycosylphosphatidylinositol (gpi) domains. oligonucleotide primers were designed according to thornton and basu […]

PMCID: 5678829
PMID: 29142828
DOI: 10.1016/j.meteno.2017.01.002

[…] homology), mdh1 (97% homology), mdh2 (94% homology), ssu1 (89% homology), and ssu2 (68% homology). for the malate dehydrogenases n-terminal targeting sequences were analyzed using a combination of signal-3l and targetp 1.1 (). the putative localization for mdh1 was the cytosol and for mdh2 the mitochondrion. the n-terminal mitochondrial targeting sequence for mdh2 was either retained […]

PMCID: 5167687
PMID: 28066334
DOI: 10.3389/fmicb.2016.01989

[…] protein for transportation out of the cytoplasm in prokaryotes (). many methods have been used for predicting signal peptides, including signalp (; ; ; ), predisi (), speplip (), signal-cf (), signal-3l (), signal-blast (), phobius (), lipop () and philius (). all the prediction methods have limited ability to discriminate between signal peptides and n-terminal transmembrane helices. […]

PMCID: 5104382
PMID: 27832149
DOI: 10.1371/journal.pone.0166274

[…] spoctopus (http://octopus.cbr.su.se/; cleavage at g58), speplip (http://gpcr.biocomp.unibo.it/cgi/predictors/spep/pred_spepcgi.cgi; cleavage at a59), signal3l (http://www.csbio.sjtu.edu.cn/bioinf/signal-3l/; cleavage at a30), emboss sigcleave (http://www.bioinformatics.nl/cgi-bin/emboss/sigcleave; cleavage at a32), and signalp (http://www.cbs.dtu.dk/services/signalp/; spi signal sequence […]


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Signal-3L institution(s)
Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China; Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China
Signal-3L funding source(s)
Supported by the Natural Science Foundation of China (NSFC Nos. 61671288, 91530321, 61603161), and Science and Technology Commission of Shanghai Municipality (No. 16JC1404300).

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