Table 4

Perl and PHP modules used in TFe

Language

Module

Purpose


Perl

CGI

Web browser interface

Perl

CGI::Session

User login

Perl

Crypt::Blowfish

Data encryption and random string generation

Perl

DBI

MySQL database interface

Perl

GD::Image

Creation of TF binding site diagrams

Perl

HTML::Detoxifier

User input filtering

Perl

Image::Resize

Image resizing and formatting

Perl

LWP::Simple

Interface between TFe and web-based APIs

Perl

pazar

Data retrieval from PAZAR

Perl

pazar::gene

Data retrieval from PAZAR

Perl

pazar::reg_seq

Data retrieval from PAZAR

Perl

TFBS::PatternGen::MEME

Creation of TF position weight matrices

PHP

dompdf 0.5.1

PDF generation


Listed on this table are the second and third party modules incorporated into TFe, with their respective programming languages, usage in TFe, and current web addresses at the time of publication.

Yusuf et al. Genome Biology 2012 13:R24   doi:10.1186/gb-2012-13-3-r24

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