TATFIND protocols

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TATFIND specifications

Information


Unique identifier OMICS_03898
Name TATFIND
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for TATFIND

TATFIND in pipelines

 (2)
2013
PMCID: 3831643
PMID: 24039236
DOI: 10.1002/mbo3.120

[…] and is not predicted to include a signal peptide for either the general secretory (sec) or twin-arginine translocation (tat) pathways (based on analyses using signalp, pred-signal, tmhmm, and tatfind). another possible explanation for the failure of strains hm26-f1 and -f2 could be the negative-charged residues of the flag-tag that are electrostatically repulsed from the membrane […]

2008
PMCID: 2442614
PMID: 18505592
DOI: 10.1186/1755-8794-1-18

[…] of domains and motifs were performed as follows: cdd [], smart [], pfam [], interpro [], prosite []. secretion signals were analyzed by signalp [,] for the secretion via the seca pathway, and tatfind for searching of the twin-arginine translocation (tat) motif of the tat pathway []. transmembrane helical segments were predicted by tmpred []. the database of bacterial lipoproteins, dolop […]


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TATFIND in publications

 (35)
PMCID: 5875014
PMID: 29598818
DOI: 10.1186/s12934-018-0901-3

[…] sequences possessing a d-score above 0.7 having a high probability that they in fact really do so []., for the identification of tat signal peptides, tatp (http://www.cbs.dtu.dk/services/tatp/ []), tatfind (http://signalfind.org/tatfind.html []), and pred-tat (http://www.compgen.org/tools/pred-tat/ []) are commonly used prediction programs. however, since twin-arginine residues can also occur […]

PMCID: 5539426
PMID: 28765221
DOI: 10.1128/mBio.00909-17

[…] at least two nucleotide changes., in each case, the h-region sequence used to calculate the score is shown underlined. for sufi, the signal peptide h-region for each variant was defined using tatfind 1.4 (, ) (http://signalfind.org/tatfind.html). for ompa and dsba, the h-region for each variant was defined using phobius () (http://phobius.sbc.su.se/). hydrophobicity was scored using […]

PMCID: 5293778
PMID: 28223967
DOI: 10.3389/fmicb.2017.00128

[…] that we used; however, they do not eliminate the transmembrane proteins in their secretome. while the secretome reported by roy et al. (), only utilized the secreted proteins by signalp followed by tatfind1.4, pred-lipo, and the application of tmhmm analysis but only in a selected subgroup of proteins. our bioinformatics pipeline could be useful to predict secretomes in other pathogen bacteria […]

PMCID: 5449189
PMID: 28513434
DOI: 10.7554/eLife.26577.032

[…] proteins were the only protein family that required both sec and tat pathways for their integration. to this end, all proteins from prokaryotic genomes available in genbank were analysed by both tatfind 1.4 () and tmhmm 2.0c () programs, initially to identify proteins with a similar n-in topology as actinobacterial rieske proteins. for each protein, both outputs were combined to identify […]

PMCID: 5158115
PMID: 27853060
DOI: 10.1264/jsme2.ME16110

[…] also required the protein to contain at least two identified peptides., the extracellular localization of the protein was assessed using signalp (), phobius (), secrotomep (), tatp (), and tatfind () programs, while ncbi, uniprot, kegg, and cog resources were used to predict protein function., the normalized spectral count (nspc) was defined as the spectral count of a protein divided […]


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TATFIND institution(s)
Department of Biology, Leidy Laboratories, University of Pennsylvania, Philadelphia, PA, USA

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