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alignments
exonerate_output
junk_trees
mrbayes_stat
orthologs
scripts
trees
EggNog.txt
PARALOGS_OF_INTERESTS.fasta
README.md
blast_output.txt
boechera_phylogenetics.pdf
own_proteins.fa

README.md

EVOLUTION ANALYSIS OF GENES ASSOCIATED WITH APOMIXIS IN BRASSICACEAE FAMILY

Authors

Rostislav Skitchenko, Mike Raiko, Vladimir Bruchin

Installing

You can clone whole repo by standart command:

git clone https://github.com/rostkick/Boechera.git

Also if you need to save it without commit-log you schould use:

git clone —depth=1 https://github.com/rostkick/Boechera.git

If you want to save only one file (for example without saving tree-plots) you should copy link of favorite file, go to https://minhaskamal.github.io/DownGit/#/home, paste it, and create Download Link.

Project description

Apomixis is an interesting object for study because of the huge potential of its use in plants selection. This phylogenetic research of several species of the Brassicaceae family was performed in order to study genes associated with asexual reproduction through seeds. The main emphasis of the work was placed on the evolution through duplications and the identifcation of paralogs responsible for apomixis-related functions.

Goals

  • Perform a comparative phylogenetics assay of the genomes of seven plants
  • Find the patterns between specific genes and apomixis plant-forms
  • Find orthologues genes in other representatives of the Brassicaceae family
  • Build the trees of genes of interests

Methods

  • Aligning proteins of interests to proteoms of 7 Brassicaceae species.
  • Multialigning of groups of proteins of interest.
  • NJ tree building.
  • MrBayes tree building.

Directories and out-dir files description

  • alignments -- contains files received from aligning orthologues groups our proteins before and after aligning
  • exonerate output -- contains dirty outputs files with prot2genome-matchs-annotations
  • junk trees -- contains prior simple NJ-proteins-trees
  • mrbayes_stat -- contains meta-information about statistical processing
  • orthologs -- containts information about orthologues groups of proteins of interests
  • scripts -- contains all scripts (python, shell) used in the project
  • trees -- contains final tree-plots, and tree-nexus-files received from MrBayes and FigTree
  • EggNog.txt -- contains information about the relationship between orthologous groups and our proteins
  • PARALOGS_OF_INTERESTS.fasta -- sequences of paralogs probably related with apomixis

Links to open-sources genomes and proteoms

Links to databases

Links to tools

Aсknowledgements

I`d like to thank everybody especially Bioinformatics Institute.

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