HMMgene statistics

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HMMgene specifications

Information


Unique identifier OMICS_01488
Name HMMgene
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline Anders Krogh <>

Publication for HMMgene

HMMgene in pipeline

2017
PMCID: 5350243
PMID: 28180967
DOI: 10.1007/s00251-017-0973-y

[…] most similar to a klra-like n-terminal region was identified approximately 4 kb upstream of cahi_klrh1 using the ncbi conserved domain database (marchler-bauer et al. ), whereas blastn, blastx, and hmmgene failed to predict this portion of the gene. despite this, both cahi_klrh1 and bota_klrh1 intriguingly form an intact open reading frame across the exons encoding the c-terminal lectin domain. […]


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HMMgene in publications

 (15)
PMCID: 5350243
PMID: 28180967
DOI: 10.1007/s00251-017-0973-y

[…] search tool (blast) against genbank and known nkc genes (altschul et al. ). exonic structure was informed using blast within ncbi against the reference rna sequence database (i.e., refseq_rna). hmmgene was additionally used to hunt for putative open reading frames (krogh )., a bac library was previously developed from a friesian dairy bull (di palma ; di palma et al. ) and was screened […]

PMCID: 4573434
PMID: 26421304
DOI: 10.1155/2015/831352

[…] ], weight matrices, the hidden markov model, the quadratic discriminant function [], and the neural network model []. the programs used for predicting splice sites based on these algorithms include hmmgene [], netgene2 [, ], geneid [], genesplicer [], and splicemachine []. , comparison analysis based on ests, mrna, and gene fragments: est comparative analysis was one of the earliest as research […]

PMCID: 5054498
PMID: 22917190
DOI: 10.1016/j.gpb.2012.02.001

[…] p = (sn + sp)/2 is used in evaluation. it is worthy noting that the values in bold face denote the superior recognitions. sn, sensitivity; sp, specificity; p, precision., note: data for genemark.hmm, hmmgene, fgenes, genie, and morgan were obtained from . for the hmr195 datasets, the hmmgene performs the best for recognition. it is worthy noting that the values in bold face denote the superior rec […]

PMCID: 3305314
PMID: 22438907
DOI: 10.1371/journal.pone.0033261

[…] are reported in ., in order to increase our confidence that nebulin repeats are specific to the lasp family in non-bilaterians, we performed the following analysis. first, we ran augustus and hmmgene on each of the non-bilaterian genomes in our study , . next, we translated these genomes in six frames. finally, we searched these hypothetical proteomes, along with the published proteomes, […]

PMCID: 3091688
PMID: 20923558
DOI: 10.1186/1471-2164-11-539

[…] functional or dysfunctional hemoglobin-like genes. specifically, the masked and unmasked sequences were analysed using the ab initio gene prediction programs genscan [], genemark [], fgenesh [] and hmmgene [], and the results of each prediction program were compared. in an attempt to identify putative psuedogenes or hemoglobin gene remnants, hmmer (v1.8.5) [] was used to scan the sequence […]


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HMMgene institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

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