ibanknatoprad / ovulgaris_saliva_proteomics

Proteomics of Octopus vulgaris saliva and salivary glands

ovulgaris_saliva_proteomics

Proteomics of Octopus vulgaris saliva and salivary glands. Subheadings refer to specific aspects of the analysis with links to scripts, notes and tools used.

Running HPC Analyses

These are contained within the folder 'hpc' and require copies of large data files. The hpc README for details on how to access these files

The proteogenomics folder within hpc contains just small files and a README. See the readme within this directory for details on running that analysis.

Distinguishing known and novel peptide with bedtools

• peptide_uniqueness.rb
• score_by_uniqueness.rb
• peptides_from_gff.rb
• filter_gff.rb

Extracting protein sequences to start with a Methionine

• finding_m.md

Sequence length between known and novel proteins

• known_novel_characteristics.Rmd

CRRF analysis of cysteine rich regions in Arachnoserver, Tox-Prot and SwissProt

• chasing_cysteines.Rmd

Obtaining protein characteristics for the protein table

• maxquant_table_prep.md

Creating the protein characteristics table, extracting putative toxin candidates and performing a the Fisher's Exact Test on cysteine rich regions and secreted sequences

• fresh_maxquant_table.Rmd

Dot product tool to match sequence amino acid composition to alpha- and beta- cephalotoxin

• aa_composition.py

Dot product frequency distributions to test for outliers

• dot_product.Rmd

Toxin domain heatmap

• heatmap_TD.Rmd

SSCR proteins heatmap

• heatmap_SSCR.Rmd

Cephalopod serine protease tree

• sp_tree5.Rmd

Serine protease tree including additional taxa and sequences

• SP_tree.Rmd