Tag: Pattern

PaGE 5.1.6 – Patterns from Gene Expression

PaGE 5.1.6

:: DESCRIPTION

PaGE (Patterns from Gene Expression) is free downloadable software for microarray analisys. PaGE can be used to produce sets of differentially expressed genes with confidence measures attached.

::DEVELOPER

the Computational Biology and Informatics Laboratory (in the Center for Bioinformatics at the University of Pennsylvania)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PaGE

:: MORE INFORMATION

Citation:

Grant G.R., Liu J., Stoeckert C.J.Jr. (2005)
A practical false discovery rate approach to identifying patterns of differential expression in microarray data,
Bioinformatics, Vol 21 no 11, 2684-2690.

doublet 1.0 – Incorporate Patterns of Dipeptide Covariation to Align Protein Sequences

doublet 1.0

:: DESCRIPTION

doublet is a modified version of the Smith-Waterman algorithm that incorporates patterns of dipeptide covariation to align protein sequences.

::DEVELOPER

Computational Genomics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  doublet

:: MORE INFORMATION

Citation:

Gavin A. Price, Gavin E. Crooks, Richard E. Green and Steven E. Brenner
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
Bioinformatics 21 (20): 3824-3831.

Pratt 2.1 – Find Flexible Patterns in Unaligned Protein Sequences

Pratt 2.1

:: DESCRIPTION

PRATT is a tool to discover patterns that are conserved in a set of protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported.

Pratt Online Version

::DEVELOPER

Inge Jonassen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Pratt

:: MORE INFORMATION

Citation

I.Jonassen, J.F.Collins, D.G.Higgins.
Finding flexible patterns in unaligned protein sequences
Protein Science 4, 1587-1595 (1995)

I. Jonassen
Efficient discovery of conserved patterns using a pattern graph.
CABIOS 13, 509-522 (1997).