Carnac 0.98 – Predict Secondary Structure for a set of Homologous RNA Sequences

Carnac 0.98

:: DESCRIPTION

Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux / MacOsX
  • C Complier

:: DOWNLOAD

Carnac

:: MORE INFORMATION

Citation

CARNAC: folding families of related RNAs
Touzet H. and Perriquet O.
Nucl. Acids Res. (2004) 32 (suppl 2): W142-W145

BSpred – Predict Binding Site of Proteins

BSpred

:: DESCRIPTION

BSpred is a neural network based algorithm for predicting binding site of proteins from amino acid sequences. The algorithm was extensively trained on the sequence-based features including protein sequence profile, secondary structure prediction, and hydrophobicity scales of amino acids.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

  BSpred

:: MORE INFORMATION

Citation

S. Mukherjee, Y. Zhang.
Protein-protein complex structure predictions by multimetic threading and template recombination.
Structure. 2011 Jul 13;19(7):955-66.

DPS 1.4.0 – Predict and Prioritize Pairs of Drugs

DPS 1.4.0

:: DESCRIPTION

DPS (Drug Pair Seeker) is a Java program that attempts to predict and prioritize pairs of drugs using the Connectivity Map dataset. Users can enter lists of up and down differentially expressed genes from their experiments to receive a ranked list of drug combinations that are predicted to either reverse or aggravate the gene expression state of the cells or tissue of interest using a simple formula.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java 

:: DOWNLOAD

 DPS

:: MORE INFORMATION

Citation

Zhong Y, Chen EY, Liu R, Chuang PY, Mallipattu SK, Tan CM, Clark NR, Deng Y, Klotman PE, Ma’ayan A, He JC.
Renoprotective effect of combined inhibition of angiotensin-converting enzyme and histone deacetylase.
J Am Soc Nephrol. 2013 Apr;24(5):801-11

N-score – Predict Nucleosome Positions from DNA Sequence information

N-score

:: DESCRIPTION

N-score is a wavelet analysis based model for predicting nucleosome positions from DNA sequence information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python/Matlab

:: DOWNLOAD

 N-score

:: MORE INFORMATION

Citation

Genomic sequence is highly predictive of local nucleosome depletion.
Yuan GC, Liu JS.
PLoS Comput Biol. 2008 Jan;4(1):e13

CRNPRED 1.1 – Predict Secondary Structures of Protein

CRNPRED 1.1

:: DESCRIPTION

CRNPRED is a program that predicts secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO) of a native protein structure from its amino acid sequence.

CRNPRED Online Version

::DEVELOPER

CRNPRED team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CRNPRED

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Sep 5;7:401.
CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks.
Kinjo AR, Nishikawa K.

newDNA-Prot – DNA Binding Protein Predict Software

newDNA-Prot

:: DESCRIPTION

newDNA-Prot will predict the DNA-binding proteins when input a protein sequence (Fasta format).

::DEVELOPER

newDNA-Prot team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • fortran-windows

:: DOWNLOAD

newDNA-Prot

:: MORE INFORMATION

Citation

newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation.
Zhang Y, Xu J, Zheng W, Zhang C, Qiu X, Chen K, Ruan J.
Comput Biol Chem. 2014 Oct;52:51-9. doi: 10.1016/j.compbiolchem.2014.09.002.

PromFD 1.0 – Predict Promoter Regions in DNA Sequences

PromFD 1.0

:: DESCRIPTION

PromFD is a computer program to recognize vertebrate RNA polymerase II promoters

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PromFD

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Feb;13(1):29-35.
PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices.
Chen QK, Hertz GZ, Stormo GD.

MiRScan 3 – Predict microRNA Genes from pairs of Conserved Sequences

MiRScan 3

:: DESCRIPTION

MiRScan is a computational procedure to identify miRNA genes conserved in more than one genome.

MiRScan Online Version

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Python

:: DOWNLOAD

 MiRScan

:: MORE INFORMATION

Citation

Genome Res. 2007 Dec;17(12):1850-64. Epub 2007 Nov 7.
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.
Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC.

The microRNAs of Caenorhabditis elegans.
Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP.
Genes Dev. 2003 Apr 15;17(8):991-1008. Epub 2003 Apr 2.

ILM 1.0 – Predict RNA Secondary Structures with Pseudoknots

ILM 1.0

:: DESCRIPTION

 ILM (Iterated Loop Matching) is a web server for predicting RNA secondary structures with pseudoknots.

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C Compiler

:: DOWNLOAD

 ILM

:: MORE INFORMATION

Citation

Ruan J, Stormo GD and Zhang W.
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots“,
Bioinformatics. 2004 Jan 1;20(1):58-66.

DriverNet 1.0.0 – Predict Functional Important Driver Genes in Cancer Genome

DriverNet 1.0.0

:: DESCRIPTION

DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package

:: DOWNLOAD

  DriverNet

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R124.
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
Bashashati A, Haffari G, Ding J, Ha G, Lui K, Rosner J, Huntsman DG, Caldas C, Aparicio SA, Shah SP.