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GlimmerHMM git repository
License: Other
Copyright (c) 2003 by Mihaela Pertea. This system is licensed as open source under the terms in the file LICENSE. GlimmerHMM system is currently trained for Arabidopsis thaliana, rice, and human. The system is already compiled for linux, 32 bit platforms. You can compile your own system for your unix platform just by typing make in the sources directory. To run GlimmerHMM just use your own compiled GlimmerHMM or the already existing pre-compiled GlimmerHMM from the bin directory.You will also need to specify the directory containing the training files. For instance, if you want to run GlimmerHMM for Arabidopsis on a linux platform you should type >GlimmerHMM/bin/glimmerhmm_linux fasta.file -d GlimmerHMM/trained_dir/arabidopsis/ To train GlimmerHMM you should first run make in the train directory. Read readme.train from GlimmerHMM/train. After creating your own training directory you can use it at the -d option with GlimmerHMM. For human predictions, if you don't know the GC isochore of your input sequence, use the usual command: >GlimmerHMM/bin/glimmerhmm_linux fasta.file -d GlimmerHMM/trained_dir/human If you already know the isochore of where the sequence is comming use directly the training directory for that isochore. There were four isochores for which GlimmerHMM was trained for human: 0-43% GC, 43-51% GC, 51-57% GC, and 57-100% GC. E.g. suppose the predicted isochore of the input sequence has a 39% GC content. The command to use for running GlimmerHMM should be: >GlimmerHMM/bin/glimmerhmm_linux fasta.file -d GlimmerHMM/trained_dir/human/Train0-43 For additional information about GlimmerHMM see http://www.cbcb.umd.edu/software/glimmerhmm/.
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