Significant random signature
Applying this method, we found a set of significant genes in breast cancer, including TAT, a gene that has never been reported as an important gene in breast cancer.
OrthoGNC
OrthoGNC (Accurate Identification of Orthologs based on Gene Neighborhood Conservation) is a software for predicting accurate pairwise orthology relations based on gene neighborhood conservation.
IMHRC
IMHRC (InterModule Hub Removal Clustering) is a graph clustering algorithm that is developed based on intermodule hub removal in the weighted graphs which can detect overlapped clusters. Due to these properties, it is especially useful for detecting protein complexes in proteinprotein interaction (PPI) networks with associated confidence values.
SIREN
The Signing of Regulatory Networks (SIREN) algorithm can infer the regulatory type (positive or negative regulation) of interactions in a known gene regulatory network given corresponding genomewide gene expression data.
PSEHMM
PSEHMM is a tool for the genomewide
CNV detection from Next Generation Sequencing data (mate pair
reads). PSEHMM applies an HMM with PositionSpecific Emission
probabilities for modeling different aberrations in the mate
pairs, after being mapped to the reference genome.
LRC (logistic regression model and clustering
approach)
A computational method based on a combination
of physicochemical and structural properties to
predict the Bcell epitopes. We model the surface of antigen with a
weighted graph, which vertices represent surface residues and edges
denote the relation between residues. For each residue, thephysicochemical
and structural properties, as well as the probability
of occurrence each of amino acid types in epitope
regions are exploited.
PEIMAN 1.0
Post translational modification, Enrichment, Integration and Matching
ANalysis (PEIMAN) is a standalone software for enrichment analysis in post
translational modification (PTM) types.
ProDomAs
( Protein Domain Assignment Server )
The ProDomAs web
server implements an automatic algorithm for protein domain assignment.
SSP
A de novo transcriptome assembler that assembles
RNAseq reads into transcripts. SSP aims to reconstructs all the
alternatively spliced isoforms and estimates the expression level of them
using interval integer linear programming .
NetAl
(Nework
Alignment)
A novel algorithm for the global alignment of
proteinprotein interaction networks.
PUTracer
(Protein
Unit
Tracer)
PUTracer is a reliable method to detect
automatically structural domains as protein units. This server provides
number of domains and domain boundary for a chain with continuesdomains.
STON
(STructure
comparisON)
Protein structure comparison is an important problem
in bioinformatics and has many applications in study of structural and
functional genomics. Most of the protein structure comparison methods give
the alignment based on minimum rmsd and ignore many significant local
alignments that may be important for evolutionary or functionally studies.
we have developed a new algorithm to find aligned
residues in two proteins with desired rmsd value. The parameterized distance
and rotation in this program enable us to search for strongly or weakly
similar aligned fragments in two proteins.
FAssign
(Fuzzy
Assignment)
A new algorithm for the protein secondary
structure assignment, using fuzzy logic based on backbone angles.
Surfield
A
knowledgebased potential of meanforce using pairwise residue contact area
RSAPRP
(Relative
Solvent Accessibility  Pace Regression Predictor)
RSAPRP
is a software to prediction of Relative solvent accessibility of amino acids from protein
sequence with evolutionary information and pace regression method. you can use a
fasta file or fasta sequence as input of program.
FullPSSM (Position 
Specific
Scoring
Matrix Software)
FullPSSM is a stand alone software for calculating positionspecific scoring matrix(PSSM) for
a given protein sequence.this software has a userfriendly interface, that
user can easily calculate PSSM for many fasta files at once.also this version
support uniref 50 ,uniref 90 and uniref 100 databases.
FixDSSP (Fix 
DSSP
Software)
FixDSSP is a stand alone software for generating dssp file for a given pdb file.this
software has a userfriendly interface, that user can easily generate dssp files
for many selected pdb files at once.
As you know ,in dssp files that generate from pdb files ,it is possible that
exists some noise in generated output(e.g. incorrect residue
number,incorrect line number and unkonwn residues).this software report these
errors to the user and have options to correct them..
FRRP
(Flexible
Rigid
Regions
Predictor)
FRRP
is a software to prediction of flexibility of amino acids from protein
sequence. For further comparison between sequence, flexibility and other
properties such as 2D Structure
and Accessibility you can use a pdb file or it's code as input of program.
PaperHap
(Partially
Perfect
Haplotype
Block
Partitioning)
This algorithm
identifies haplotype block partitions, useing a set of three parameters.
GPMAP
(
Global Haplotype
Partitioning
for
Maximal
Associated SNP
Pairs)
GPMAP has been developed based on the
open source code of
Haploview (ver. 4.1).
Therefore GPMAP basically inherits all Haploview functions plus the
global haplotype partitioning method
(Ref).
ASILA
()
ASILA is written in g++ (MinGW3.1). It gets M (
number of different haplotypes ) and N ( Number
of SNP ) as an input and
generate all perfect
phylogeny matrices with M different rows and N columns. As the number of
these matrices is exponential,
run time of this
program is exponential.
LIBRA
()
This software is for detecting similar patterns called
Motif on DNA sequences
MC.Net
()
Phylogenetic networks are a generalization of phylogenetic
trees that allow the representation of conflicting signals or alternative
evolutionary histories in a single diagram. There are several methods for
constructing these networks. MCNet is A method for the construction of
phylogenetic networks based on MonteCarlo method. MCNet finds a circular
ordering for taxa, based on MonteCarlo with simulated annealing, it then
extracts splits from the circular ordering and uses nonnegative least
squares for weighting splits. One can use SplitsTree program to draw
phylogenetic networks from weighted splits.
MCQ.Net
()
MCQNet is a heuristic algorithm based on the simulated
annealing as a method for constructing phylogenetic networks from weighted
quartets.
CLUSMO
CLUSMO is written in MATLAB. It gets simulated data and
initial parameters as inputs. This algorithm applied for estimating
parameters of A Profile Hidden Markov Models.
RaPPer
This program will generate random perfect phylogeny matrix
with following conditions.
The results will be send to your email.
TripNet
TripNet is an algorithm for constructing phylogenetic
networks from sparse sets of rooted triplets.
SNSA
Different partial phylogenetic trees can be derived from
different evidences and different methods. One important problem is to
summarize these partial phylogenetic trees using a supernetwork. SNSA (SuperNetworkSimulated
Annealing) is a method to construct a supernetwork from partial trees based
on simulated annealing.
LSPC
LSPC is written in R. It gets simulated data and real data
as inputs. This algorithm applied for learning the skeleton of BN.
SwInt
Some Description about SwInt ...
IPCACMI
IPCACMI algorithm is written
in Matlab. It gets simulated data and real data as
inputs. This algorithm applied for learning the skeleton of BN.
CN
In
order to quantitatively evaluate the performance of the CN algorithm,
we use simulated dataset which generated from Dream3 (Dialogue for Reverse
Engineering Assessments and Methods) size of 10, 50 and 100 and real dataset
(SOS DNA repair network with experiment data set in Escherichia coli).
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