| ♣ Multiple Sequence Analysis |
| PRALINE |
Multiple sequence alignment toolkit with several
strategies to optimise alignment quality |
| VerAlign |
Compare a test alignment against a reference alignment
on the basis of Column and Sum-of-Pairs score assessment |
| ConvertAlign |
Convert your alignment to other alignment formats
|
| Sequence Harmony |
Detection of subfamily specific functional sites from a multiple sequence alignment by an entropy-based scoring function. |
| Multi-RELIEF |
Detection subfamily specific functional sites from a multiple sequence alignment by RELIEF-based feature selection. |
|
| ♣ Pairwise Sequence Alignment |
| ALICAO |
Contact-based sequence alignment between query sequence
(unknown structure) and template sequence (known structure) |
| AuberGene |
A genome alignment program which explores the idea of transitivity of local alignments |
|
| ♣ Phylogeny |
| PhyloPars |
PhyloPars takes an incomplete feature matrix and a phylogeny as input and estimates the missing parameter values |
|
| ♣ Databases & Matrices |
| CAO |
Contact-based substitution matrices |
| LinkerDB |
Database for searching and visualising protein inter-domain linkers |
|
| ♣ Array Data Analysis |
| aCGH-smooth |
A "smoothing" algorithm that adjusts the observed array-CGH
values such that they represent the copy number of the most common tumor cells |
| CGHnormaliter |
Normalization of dual-channel aCGH data displaying imbalanced aberrations |
| MaRe |
Microarray Retriever (MaRe) enables batch retrieval
from GEO and ArrayExpress microarray repositories |
| Fuzzy clustering |
Fuzzy clustering of array CGH data, taking overlapping clusters and outliers into account |
|
| |
| ♣ Protein Secondary Structure Prediction |
| YASPIN |
HMM based neural network secondary structure prediction using PSI-BLAST PSSM matrices
|
| SymPRED |
Consensus secondary structure prediction using dynamic
programming for optimal segmentation or majority voting |
|
| ♣ Protein Analysis |
| DOMAIN3D |
Identifies globular domains in protein structure |
| DOMAINATION
| Domain prediction based on sequence similarity searching |
| SCOOBY-DOmain
| Domain prediction based on protein sequence |
| webPRC |
The Profile Comparer for alignment-based searching of public domain databases |
| REPRO |
Identifies protein sequence repeats using a
graph-based iterative clustering procedure |
| TRUST |
Repeats detection analysis |
|
| ♣ RNA |
| K2N |
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal |
| SPuNC |
Structure Prediction using Nucleotide Composition |
|
| ♣ Downloads |
| You can download bioinformatics software, source codes and
substitution matrices, produced by the IBIVU Centre |
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