SCHOOL OF BIOLOGICAL SCIENCES

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 (Inter-Module Hub Removal Clustering) is a graph clustering algorithm that is developed based on inter-module hub removal in the weighted graphs which can detect overlapped clusters. Due to these properties, it is especially useful for detecting protein complexes in protein-protein 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 genome-wide gene expression data.

PSE-HMM

PSE-HMM is a tool for the genome-wide CNV detection from Next Generation Sequencing data (mate pair reads). PSE-HMM applies an HMM with Position-Specific 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 B-cell 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 RNA-seq 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 protein-protein 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 continues-domains.

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 knowledge-based potential of mean-force using pairwise residue contact area

RSA-PRP       (Relative Solvent Accessibility - Pace Regression Predictor)

RSA-PRP 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.

Full-PSSM     (Position - Specific Scoring Matrix Software)

Full-PSSM is a stand alone software for calculating position-specific 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.

Fix-DSSP     (Fix - DSSP Software)

Fix-DSSP 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++ (MinGW-3.1). 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. MC-Net is A method for the construction of phylogenetic networks based on Monte-Carlo method. MC-Net finds a circular ordering for taxa, based on Monte-Carlo with simulated annealing, it then extracts splits from the circular ordering and uses non-negative least squares for weighting splits. One can use SplitsTree program to draw phylogenetic networks from weighted splits.

MCQ.Net     ()

MCQ-Net 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 (SuperNetwork-Simulated 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 ...

IPCA-CMI

IPCA-CMI 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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