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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 http://www.ebi.ac.uk/Tools/psa/
Splice site prediction, determining splice site strength and confidence level SpliceView http://bioinfo.itb.cnr.it/oriel/splice-view.html
Neural Network http://www.fruitfly.org/seq_tools/splice.html
NetGene 2 http://www.cbs.dtu.dk/services/NetGene2
ESE-Finder http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi
Human Splicing Finder (HSF) version 2.4 http://www.umd.be/HSF
Finding splicing enhancers and splicing silencers ESE-Finder http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi
Human Splicing Finder (HSF) version 2.4 http://www.umd.be/HSF
mRNA sequence conversion to protein Translator http://www.fr33.net/translator.php
Calculating Molecular weight and pI of protein ExPASY ‘Compute pI/MW tool’ http://web.expasy.org/compute_pi/
Predicting sub-cellular localization of proteins ProtComp v. 9.0 http://linux1.softberry.com/berry.phtml?topic=protcompan&group=programs&subgroup=proloc
Prediction of 3D structure and determination of homology index Phyre2 http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index