The SeqProp Class

Introduction

This section will give an overview of the methods that can be executed for a single protein sequence.

notebooks/SeqProp*

Function	Description	Internal Python class used and functions provided	External software to install	Web server
Secondary structure and solvent accessibilities	Predictions of secondary structure and relative solvent accessibilities per residue	`scratch module <ssbio.protein.sequence.properties.scratch>`	`instructions/scratch`
Thermostability	Free energy of unfolding (ΔG), adapted from Oobatake (Oobatake & Ooi 1993) and Dill (Dill et al. 2011)	`thermostability module <ssbio.protein.sequence.properties.thermostability>`
Transmembrane domains	Prediction of transmembrane domains from sequence	`tmhmm module <ssbio.protein.sequence.properties.tmhmm>`	`instructions/tmhmm`
Aggregation propensity	Consensus method to predict the aggregation propensity of proteins, specifically the number of aggregation-prone segments on an unfolded protein sequence	`aggregation_propensity module <ssbio.protein.sequence.properties.aggregation_propensity>`		`instructions/amylpred`

Function	Description	Internal Python class used and functions provided	External software to install	Web server	Alternate external software to install
Various sequence properties	Basic properties of the sequence, such as percent of polar, non-polar, hydrophobic or hydrophilic residues.	Biopython ProteinAnalysis `sequence residues module <ssbio.protein.sequence.properties.residues>`			`instructions/emboss` pepstats
Sequence alignment	Basic functions to run pairwise or multiple sequence alignments	Biopython pairwise2 `alignment module <ssbio.protein.sequence.utils.alignment>`			`instructions/emboss` needle

ssbio.protein.sequence.seqprop