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Glossary
Analysis Scripts -- Under Construction
Software Tools
- PaGE
PaGE is free downloadable Perl software (tested mainly on Unix
systems) which can be used as a statistical test for differentially
expressed genes between two experimental conditions, given replicated
experiments. These lists are generated using the False Discovery
Rate method of controlling the false positives.
- TESS
TESS is a web tool for predicting transcription factor binding
sites in DNA sequences. It can identify binding sites using
site or consensus strings and positional weight matrices from
the TRANSFAC, IMD, and our CBIL-GibbsMat database. You may also
include your own site or consensus strings and/or weight matrices
in the search.
- Prediction of Golgi localised transmembrane proteins
This program uses a new method to predict Golgi membrane proteins
based on their transmembrane domains. Yuan Z, Teasdale RD. Reference:
Prediction of Golgi Type II membrane proteins based on their
transmembrane domains. Bioinformatics. 2002 Aug;18(8):1109-15.
- SVMtm: Support Vector Machines to predict transmembrane domains
This program uses SVM machine-learning to predict the presence of transmembrane
domains in full length open reading frames.
- MoSearch
This web tool is to search the membrane topology predictions for the human and mouse
proteomes, based on the pipeline described in Kanapin et al,
2003). Predictions can be accessed using accession numbers or
BLAST analysis for all mouse RIKEN RPS, IPI and human IPI full length ORFs.
Publications
Online Journals
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