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)
The automatic assignment of the protein secondary structure from three
dimensional coordinates is an essential step in the characterization of
protein structure. There are several methods for assigning secondary
structure from the three-dimensional structure based on different
definitions. We developed a new algorithm for the protein secondary
structure assignment, using fuzzy logic based on backbone angles. In this
method, we assign a non negative number ranging from zero to one hundred to
each residue to express the membership degree for being in a helix or beta
strand. This method can be converted to the classical methods whenever we
assume that any residue with membership degree greater than a selected
cutoff be in a helix or beta strand structure. Comparison of the results
with structures reported in PDB, DSSP and STRIDE for 4843 proteins show that
our algorithm works as well as other classical methods. Also using fuzzy
assignment in protein structural alignment, can lead us to an accurate
results. FAssign is an online tool with a user-friendly interface, for
assignment of proteins based on fuzzy assignment method (http://bioinf.cs.ipm.ir/softwares/fassign).
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.
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