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Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Krogh A, et al. J Mol Biol. 2001 Jan 19;305(3):567-80. doi: 10.1006/jmbi.2000.4315. J Mol Biol. 2001. PMID: 11152613
We describe and validate a new membrane protein topology prediction method, TMHMM, based on a hidden Markov model. We present a detailed analysis of TMHMM's performance, and show that it correctly predicts 97-98 % of the transmembrane helices. ...A TMH …
We describe and validate a new membrane protein topology prediction method, TMHMM, based on a hidden Markov model. We present …
BayesMD: flexible biological modeling for motif discovery.
Tang MH, Krogh A, Winther O. Tang MH, et al. J Comput Biol. 2008 Dec;15(10):1347-63. doi: 10.1089/cmb.2007.0176. J Comput Biol. 2008. PMID: 19040368
We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. ...In a similar fashion we train organism-specific priors for the …
We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori k …
Sampling realistic protein conformations using local structural bias.
Hamelryck T, Kent JT, Krogh A. Hamelryck T, et al. PLoS Comput Biol. 2006 Sep 22;2(9):e131. doi: 10.1371/journal.pcbi.0020131. Epub 2006 Aug 21. PLoS Comput Biol. 2006. PMID: 17002495 Free PMC article.
The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates …
The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure …
Large-scale prokaryotic gene prediction and comparison to genome annotation.
Nielsen P, Krogh A. Nielsen P, et al. Bioinformatics. 2005 Dec 15;21(24):4322-9. doi: 10.1093/bioinformatics/bti701. Epub 2005 Oct 25. Bioinformatics. 2005. PMID: 16249266
Genome comparison either on a large or small scale would be facilitated by using a single standard for annotation, which incorporates a transparency of why an open reading frame (ORF) is considered to be a gene. RESULTS: A total of 143 prokaryot …
Genome comparison either on a large or small scale would be facilitated by using a single standard for annotation, which incor …
On the accuracy of short read mapping.
Menzel P, Frellsen J, Plass M, Rasmussen SH, Krogh A. Menzel P, et al. Methods Mol Biol. 2013;1038:39-59. doi: 10.1007/978-1-62703-514-9_3. Methods Mol Biol. 2013. PMID: 23872968
In a single experiment, millions of reads are produced. To gain knowledge from these experiments the first thing to be done is finding the genomic origin of the reads, i.e., mapping the reads to a reference genome. ...Furthermore, we provide simple statistical resul …
In a single experiment, millions of reads are produced. To gain knowledge from these experiments the first thing to be done is findin …
Bias of purine stretches in sequenced chromosomes.
Ussery D, Soumpasis DM, Brunak S, Staerfeldt HH, Worning P, Krogh A. Ussery D, et al. Comput Chem. 2002 Jul;26(5):531-41. doi: 10.1016/s0097-8485(02)00013-x. Comput Chem. 2002. PMID: 12144181
Using this criteria, a random sequence would be expected to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tracts. ...One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokary …
Using this criteria, a random sequence would be expected to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tr …
RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.
Petersen L, Larsen TS, Ussery DW, On SL, Krogh A. Petersen L, et al. J Mol Biol. 2003 Mar 7;326(5):1361-72. doi: 10.1016/s0022-2836(03)00034-2. J Mol Biol. 2003. PMID: 12595250
The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved -35 region, but shows a very strong periodic variation in the AT-content and semi-conserved T-stretches, with …
The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not conta …
An evolutionary method for learning HMM structure: prediction of protein secondary structure.
Won KJ, Hamelryck T, Prügel-Bennett A, Krogh A. Won KJ, et al. BMC Bioinformatics. 2007 Sep 21;8:357. doi: 10.1186/1471-2105-8-357. BMC Bioinformatics. 2007. PMID: 17888163 Free PMC article.
Therefore, we have developed a method for evolving the structure of HMMs automatically, using Genetic Algorithms (GAs). RESULTS: In the GA procedure, populations of HMMs are assembled from biologically meaningful building blocks. ...
Therefore, we have developed a method for evolving the structure of HMMs automatically, using Genetic Algorithms (GAs). RESULTS: In t …
A hidden Markov model approach for determining expression from genomic tiling micro arrays.
Munch K, Gardner PP, Arctander P, Krogh A. Munch K, et al. BMC Bioinformatics. 2006 May 3;7:239. doi: 10.1186/1471-2105-7-239. BMC Bioinformatics. 2006. PMID: 16672042 Free PMC article.
RESULTS: We present a probabilistic procedure, ExpressHMM, that adaptively models tiling data prior to predicting expression on genomic sequence. A hidden Markov model (HMM) is used to model the distributions of tiling array probe scores in expressed and non-express …
RESULTS: We present a probabilistic procedure, ExpressHMM, that adaptively models tiling data prior to predicting expression on genom …
EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance.
Larsen TS, Krogh A. Larsen TS, et al. BMC Bioinformatics. 2003 Jun 3;4:21. doi: 10.1186/1471-2105-4-21. Epub 2003 Jun 3. BMC Bioinformatics. 2003. PMID: 12783628 Free PMC article.
RESULTS: In this paper, we present a new automated gene-finding method, EasyGene, which estimates the statistical significance of a predicted gene. The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome …
RESULTS: In this paper, we present a new automated gene-finding method, EasyGene, which estimates the statistical significance of …
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