MAKER Tutorial 2013
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Contents
About MAKER
MAKER is an easy-to-use genome annotation pipeline designed for small
research groups with little bioinformatics experience. However, MAKER is
also designed to be scalable and is thus appropriate for projects of any
size including use by large sequence centers. MAKER can be used for de
novo annotation of newly sequenced genomes, for updating existing
annotations to reflect new evidence, or just to combine annotations,
evidence, and quality control statistics for use with other GMOD
programs like GBrowse,
JBrowse,
Chado, and
Apollo.
MAKER has been used in many genome annotation projects:
- Schmidtea mediterranea - planaria (A Alvarado, Stowers Institute)
PubMed
- Pythium ultimum oomycete (R Buell, Michigan State Univ.)
PubMed
- Pinus taeda - Loblolly pine (A Stambolia-Kovach, Univ. California
Davis) PubMed
- Atta cephalotes - leaf-cutter ant (C Currie, Univ. Wisconsin,
Madison) PubMed
- Linepithema humile - Argentine ant (CD Smith, San Francisco State
Univ.) PubMed
- Pogonomyrmex barbatus - red harvester Ant (J Gadau, Arizona State
Univ.) PubMed
- Conus bullatus - cone snail (B Olivera Univ. Utah)
PubMed
- Petromyzon marinus - Sea lamprey (W Li, Michigan State)
PubMed
- Fusarium circinatum - pine pitch canker (B Wingfield, Univ.
Pretoria) - Manuscript in preparation
- Cardiocondyla obscurior - tramp ant (J Gadau, Arizona State Univ.) -
Manuscript in preparation
- Columba livia - pigeon (M Shapiro, Univ. Utah) - Manuscript in
preparation
- Megachile routundata alfalfa leafcutter bee () - Manuscript in
preparation
- Latimeria menadoensis - african coelacanth () -
PubMed
- Nannochloropsis - micro algae (SH Shiu, Michigan State Univ.)
PubMed
- Arabidopsis thale cress re-annotation (E Huala, TAIR) - Manuscript
in preparation
- Cronartium quercuum - rust fungus (JM Davis, Univ. Florida) -
Annotation in progress
- Ophiophagus hannah - King cobra (T. Castoe, Univ. Colorado) -
Annotation in progress
- Python molurus - Burmese python (T. Castoe, Univ. Colorado) -
Annotation in progress
- Lactuca sativa - Lettuce (RW Michelmore) - Annotation in progress
- parasitic nematode genomes (M Mitreva, Washington Univ)
- Diabrotica virgifera - corn rootworm beetle (H Robertson, Univ.
Illinois)
- Oryza sativa - rice re-annotation (R Buell, MSU)
- Zea mays - maize re-annotation (C Lawrence, MaizeGDP)
- Cephus cinctus - wheat stem sawfly (H Robertson, Univ. Illinois)
- Rhagoletis pomonella - apple maggot fly (H Robertson, Univ.
Illinois)
Introduction to Genome Annotation
What Are Annotations?
Annotations are descriptions of different features of the genome, and
they can be structural or functional in nature.
Examples:
Genome project from sequencing to experimental application of
annotations
Genome sequence itself is not very useful. The first question that
occurs to most of us when a genome is sequenced is, “where are the
genes?” To identify the genes we need to annotate the genome. And while
most researchers probably don’t give annotations a lot of thought, they
use them everyday.
Examples of Annotation Databases:
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