HMMTOP protocols

HMMTOP specifications


Unique identifier OMICS_04185
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes


  • person_outline Istvan Simon <>

Publication for HMMTOP

HMMTOP IN pipelines

PMCID: 5787101
PMID: 29410672
DOI: 10.3389/fpls.2017.02156

[…] cdna of boalmt1 was amplified with sense primer 5′-atggagaaagtgagagagatagtgag-3′ and anti-sense primer 5′-tcaaatctgaagtatacgaacaccc-3′, and then constructed into the pmd18-t vector (takara, japan). hmmtop was used for transmembrane protein prediction analysis. multiple amino acid alignment was conducted by using clustalx and mega4.1 software., boalmt1 expression was evaluated using quantitative […]

PMCID: 4933719
PMID: 27458469
DOI: 10.3389/fpls.2016.00985

[…] (mw) of protein ( was calculated using compute pi/mw tool (bjellqvist et al., 1993, 1994). transmemebrane helices and topology of proteins were predicted using hmmtop (; tusnády and simon, 1998, 2001). the secondary structures of cfcyp93b and cfcyp706c were calculated using […]

PMCID: 3360030
PMID: 22655039
DOI: 10.1371/journal.pone.0037340

[…] acid and h represents any hydrophobic residue. these motifs are involved in atp binding and are common to atpases, which is indicative of their function in the abc transporter. in addition, the hmmtop server [27] predicts seven transmembrane helices for all of the znub proteins except that of znub from the second gene cluster in ca. liberibacter asiaticus, in which only six are predicted. […]

PMCID: 3155973
PMID: 21860605
DOI: 10.1155/2011/878973

[…] the sequences against hmm profiles in the pfama database (version 21.0) [8] which consists of 8957 families by using standalone version of hmmpfam of the hmmer suite [28] with e-value cutoff 0.1. , hmmtop [29] server was used for transmembrane helix prediction, and a standalone version of coils [30] program was used for coiled-coil region prediction. we used psi-blast [5] (with three iterations […]

PMCID: 1781495
PMID: 17257055
DOI: 10.1371/journal.pgen.0030017

[…] and adjusted manually (see dataset s1). because the alignment of the protein sequence c-terminal to exon 5 was ambiguous, kyte-doolittle hydropathy plots and the hidden markov modeling program hmmtop [53] were used to confirm the alignment of the transmembrane domain of exon 7. exons 6 through 9 were omitted from the phylogenetic analysis. phylogenetic relationships were then determined […]

HMMTOP institution(s)
Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary

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