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HMM-FRAME specifications


Unique identifier OMICS_14517
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA sequence, a profile HMM, and a sequencing error model.
Output data An optimal alignment between the DNA sequence and a profile HMM, as well as error positions in r.
Operating system Unix/Linux, Mac OS
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Yanni Sun

Publication for HMM-FRAME

HMM-FRAME citations


A sensitive short read homology search tool for paired end read sequencing data

BMC Bioinformatics
PMCID: 5657049
PMID: 29072140
DOI: 10.1186/s12859-017-1826-2

[…] in identifying domains. thus, it is also widely adopted for profile homology search in a number of existing ngs analysis pipelines or websites (e.g. img/m [], ebi metagenomics portal [], comet [], hmm-frame [], salt [], sat-assembler [], etc.). however, hmmer is not optimized for short-read homology searches. short reads sequenced from regions of low conservation tend to be missed. one example […]


Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

BMC Genomics
PMCID: 5103448
PMID: 27832738
DOI: 10.1186/s12864-016-3080-9

[…] presence of the diagnostic residues/motifs in the homeodomain as well as in the flanking regions. frameshift errors in lottia cf. kogamogai hox1/hox2/post-1/post-2 sequences were corrected using the hmm-frame program []. all the sequences were then manually edited with the program aliview []. the phylogenetic analysis was carried out using mrbayes v3.2.6 [] with jones-taylor-thornton model […]


A Doubling of Microphytobenthos Biomass Coincides with a Tenfold Increase in Denitrifier and Total Bacterial Abundances in Intertidal Sediments of a Temperate Estuary

PLoS One
PMCID: 4427305
PMID: 25961719
DOI: 10.1371/journal.pone.0126583

[…] formatted version of the rdp training set (v.9)., prior to alignment, the nirk/nirs gene sequence data were checked for the presence of specific functional/conserved regions and screened using the hmm frame algorithm [] included in the funframe pipeline [] to detect and correct frameshift errors. the obtained hmm alignment scores were used for further quality filtering. the cytochrome d1 hmm […]


Pyrosequencing Revealed SAR116 Clade as Dominant dddP Containing Bacteria in Oligotrophic NW Pacific Ocean

PLoS One
PMCID: 4304780
PMID: 25615446
DOI: 10.1371/journal.pone.0116271

[…] the allowed number of maximum homopolymers was 6. all reads <350 bp or >450 bp were removed. the flowgram data were then denoised []. frameshift errors were corrected using the program hmm-frame []. among the resulting reads, those without a reverse primer and those <330 bp were removed. in addition, reads were translated into amino acids, and any sequences possessing nonsense […]


Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN

Front Microbiol
PMCID: 3927136
PMID: 22558000
DOI: 10.3389/fmicb.2014.00034

[…] there are methods available to specifically correct frameshift errors in functional gene pyrosequencing datasets, such as the framebot tool ( and hmm-frame (weisman et al., ). correcting the frameshift errors in pyrosequencing datasets is particularly important for calculating otus or phylogenetic distances based on amino acid sequences. […]

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HMM-FRAME institution(s)
Computer Science and Engineering Department, Michigan State University, East Lansing, MI, USA

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