Using GlimmerM to Find Genes in Eukaryotic Genomes

互联网2013-12-31

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Abstract
Table of Contents
Figures
Literature Cited

Abstract

GlimmerM is a eukaryotic gene finder that has been used in the annotation of the genomes of Plasmodium falciparum (the malaria parasite), the model plant Arabidopsis thaliana, Oryza sativa (rice), the parasite Theileria parva, and the fungus Aspergillus fumigatus. A unique feature of the system compared to other eukaryotic gene finders is a module that allows users to provide their own data and train GlimmerM for any organism.

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Basic Protocol 1: Running GlimmerM Locally to Identify Genes
Support Protocol 1: Training GlimmerM for a Specific Organism
Alternate Protocol 1: Running GlimmerM VIA the WEB
Guidelines for Understanding Results
Commentary
Literature Cited
Figures
Tables

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Materials

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Figures

Figure 4.4.1 Training GlimmerM for a malaria data set, where the DNA sequences for training are in the file seqs.fasta and the exon coordinates are in the file exons.coord (shown on the first and second lines). By adding the text >& messages at the end of the trainGlimmerM command, the authors created a file called messages , which captured any potential messages of the training program that were normally printed on the screen. The computer prompt shown is /predator/mpertea/Malaria/train/train11_01 . The third line shows the execution of the ls command ( APPENDIX ), which lists the contents of the directory (fourth line). The directory now contains the subdirectory TrainGlimmM2001‐11‐09D14:34:57 , and the two files TrainGlimmM2001‐11‐09D14:34:57.log and messages .

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Figure 4.4.2 Example of config_file . Refer to Table for parameters.

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Figure 4.4.3 An example log file generated by trainGlimmerM .

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Figure 4.4.4 Example of false.nofilter.acc file.

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Figure 4.4.5 Example of false.nofilter.don file.

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Figure 4.4.6 Example of using the GlimmerM Web server.

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Figure 4.4.7 Output of GlimmerM Web Server.

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Figure 4.4.8 Sample output from the malaria‐specific version of GlimmerM. The FASTA file used to generate this output is available on the Current Protocols Web site (http://www3.interscience.wiley.com/c_p/cpbi_sampledatafiles.htm).

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Figure 4.4.9 Sample output of the current version of GlimmerM created by the . The FASTA file used to generate this output is available on the Current Protocols Web site (http://www3.interscience.wiley.com/c_p/cpbi_sampledatafiles.htm).

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Literature Cited

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Key References
	Salzberg et al., 1999. See above.
	This paper introduces the GlimmerM method initially used in finding genes in Plasmodium falciparum. This paper also describes how GlimmerM was used in the annotation of chromosome 2 of P. falciparum.
Internet Resources
	http://www.tigr.org/software/glimmerm/
	GlimmerM Web site.
	http://www.tigr.org/tdb/edb2/pfa1/htmls/
	A preliminary annotation of chromosomes 10, 11, and 14 of P. falciparum. (This will change when the P. falciparum genome is completed.)