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Table 3 Softwares used for the computational analysis of transcripts and proteins

From: Down regulation of KLK7 expression in breast tissues and identification of a novel spliced KLK7 mRNA

Purpose Softwares used Available at:
Sequence alignment analysis EMBOSS Pairwise Alignment Algorithms
Splice site prediction, determining splice site strength and confidence level SpliceView
Neural Network
NetGene 2
Human Splicing Finder (HSF) version 2.4
Finding splicing enhancers and splicing silencers ESE-Finder
Human Splicing Finder (HSF) version 2.4
mRNA sequence conversion to protein Translator
Calculating Molecular weight and pI of protein ExPASY ‘Compute pI/MW tool’
Predicting sub-cellular localization of proteins ProtComp v. 9.0
Prediction of 3D structure and determination of homology index Phyre2