|
|
|
|
|
Notredame's Lab Comparative Bioinformatics |
|
|
|
|
|
WELCOME!
Welcome to the Comparative Bionformatics Group Homepage(aka Notredame's lab) a research group of the Center for Genomic Regulation in Barcelona. The main focus of our group is the development of novel algorithms for the comparison of multiple biological sequences. Multiple comparisons have the advantage of precisely revealing evolutionary traces, thus allowing the identification of functional constraints imposed on the evolution of biological entities. Most comparisons are currently carried out on the basis of sequence similarity. Our goal is to extend this scope by allowing comparisons based on any relevant biological signal such as sequence homology, structural similarity, genomic structure, functional similarity and more generally any signal that may be identified within biological sequences. Using such heterogeneous signals serves two complementary purposes: (i) producing better models that take advantage of the signal evolutionary resilience, (ii) improving our understanding of the evolutionary processes that lead to the diversification of biological functions. All the applications related to our work are provided to the community through an international network of web servers that can be accessed from server.tcoffee.org.
|
|
|
|
|
|
T-Coffee |
A Multiple Sequence Alignment Package (inc. regressive mode) |
homepage |
ppt |
server |
|
Unistrap |
Bootstrap replicates taking MSA unstability into account |
homepage |
ppt |
server |
|
TCS |
Evaluation and filtering of multiple Sequence Alignments |
homepage |
ppt |
server |
|
M-Coffee |
Combination of Multiple Sequence Alignment Packages |
homepage |
ppt |
server |
|
3D-Coffee/Expresso |
Combination of Sequences and Structures |
homepage |
ppt |
server |
|
R-Coffee |
RNA Multiple Sequence Alignment |
homepage |
ppt |
server |
|
Sara-Coffee |
RNA Multiple Sequence Alignment Using Structural Information |
homepage |
|
T-RMSD |
T-RMSD Structure based clustering |
homepage |
ppt |
|
|
MOCCA |
Repeat Discovery with T-Coffee |
homepage |
|
|
SAGA and Coffee |
Multiple Protein Alignment by Genetic Algorithm |
homepage |
ppt |
|
|
(P)RAGA |
RNA Alignment by Genetic Algorithm |
homepage |
ppt |
|
|
Blast-R |
Fast and accurate database searches for non-coding RNAs |
homepage |
|
|
|
Strike |
A sequence alignment scoring tool |
homepage |
|
|
|
Pro-Coffee |
Aligns homologous promoter regions |
homepage |
|
|
|
Nextflow |
Data-driven computational toolkit for highly scalable pipelines |
homepage |
|
|
|
|
|
|
|
Courses and Lectures |
[web] |
Workshops |
[web] |
|
|
|
The Medline list of the lab's publications is available on [Medline].
|
Some of our papers are available as [PDF preprints]
|
My PhD
[ps]
[pdf]
|
|
|
|
|
T-Coffee |
Multiple Sequence Alignments Online |
Github |
Repository where you can download T-Coffee source code |
Alignment Links |
Structure and Sequence Alignment Packages |
Books |
My Favorite Scientific Books |
Dummies |
Bioinformatics For Dummies Links |
Trees |
THE site for phylogeny |
EMBnet |
Online Tools at the Swiss EMBnet |
ExPasy |
SwissProt Home |
|
|
|
*******************************************
Dr. Cedric Notredame, PhD.
Group Leader
Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Center for Genomic Regulation (CRG)
Dr Aiguader, 88
08003 Barcelona
Spain
Email: cedric.notredame@gmail.com
HOME : http://www.tcoffee.org/homepage.html
GROUP: CRG
Phone : +34 933 160 271
*******************************************
|
|
|
|
|