synthaser

Welcome to synthaser’s documentation!

synthaser is a tool for the characterisation and classificiation of the domain architecture of protein sequences. It leverages the NCBI’s conserved domain (CD) search tool, CD-Search, for comphrehensive, fully remote domain searches, and automatically characterises and classifies sequences based on user-defined rules.

To view an example of what synthaser can produce, click the image below:

Features

• Fully remote searches using the NCBI’s CD-Search API
• Automatic characterisation and classification of protein sequences based on user-defined rules
• Fully interactive visualisations which can be tweaked and saved to SVG

User guide

Get started using synthaser.

• User guide
  • Installation
    • Python version
    • Dependencies
    • Other dependencies
    • Installation
    • Installing RPS-BLAST and rpsbproc
  • Quickstart
    • Pre-search configuration using the config module
    • Running a synthaser search using the search module
    • The synthaser plot
  • Creating custom rule sets
    • Identifying domain ‘islands’
    • Creating domain types
    • Creating classification rules
    • Classification rule evaluation hierarchy
    • Using the rule file
  • Miscellaneous modules
    • getdb
    • getseq
    • extract
    • genbank

API Documentation

The following pages detail all synthaser modules.

• API Documentation
  • synthaser.classify
  • synthaser.fasta
  • synthaser.grouping
  • synthaser.models
  • synthaser.ncbi
  • synthaser.plot
  • synthaser.results
  • synthaser.rpsblast
  • synthaser.search

Indices and tables

• Index
• Module Index
• Search Page