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

Applied Cancer Research

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

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
Finding splicing enhancers and splicing silencers	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