Python Sequence Analysis Tools

This documents a set of tools, written for use in Python and using extensively the tools from the BioPython suite. It is intended not for genomic studies, but rather, for characterizing relatively short complete or RACE sequences that are expected to be based on an “expected” sequence but that nevertheless have significant sequence and/or length heterogeneity. We use the tools to study in vitro transcribed RNAs.
(another tool you may find useful is “Oligo Design“)

Author: Craig Martin
Documentation last updated: Mar 09, 2020 (v5.3)


This document describes a suite of Python tools for analysis of in vitro RNA-Seq data (not intended for genomic analyses). The basic usage follows an object oriented model. You start by defining a variable to contain information about a specific experimental data set.

myExptSetUp = Seqsetup(



Filter (“get”) Functions

These functions return a subset of the sequences, depending on specific criteria. They do not modify the sequences returned, they just remove some.