Tag: Predict

piRNApredictor 1.0 – Predict piRNA Sequences

piRNApredictor 1.0

:: DESCRIPTION

piRNApredictor is a software for predicting piRNA sequences.Identifying piwi-interacting RNAs (piRNAs) of non-model organisms is a difficult problem because piRNAs lack conservative secondary structure motifs and sequence homology between different species. In literatures, a method based on position-specific base usage was proposed to predict piRNAs with the support of genome data. For organisms without genome data, an efficient computational method is urgently required to identify and characterize their piRNAs. In this software, a k-mer method is used to identify piRNA sequences, and it performs with a precision of over 90% and a sensitivity of over 60%.

::DEVELOPER

State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology,Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • MatLab

:: DOWNLOAD

  piRNApredictor

:: MORE INFORMATION

Citation:

Zhang Y, Wang XH, Kang L.
A k-mer scheme to predict piRNAs and characterize locust piRNAs.
Bioinformatics. 27(6)771-776.

DBS-PSSM v3 – Predicts DNA-binding sites in Proteins

DBS-PSSM v3

:: DESCRIPTION

DBS-PSSM is a web server to provide predictions of DNA-binding sites for any new protein from its amino acid sequence.

::DEVELOPER

Shandar Ahmad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 Feb 19;6:33.
PSSM-based prediction of DNA binding sites in proteins.
Ahmad S, Sarai A.

CisPlusFinder 1.0 – Predict Cis-regulatory modules

CisPlusFinder 1.0

:: DESCRIPTION

 CisPlusFinder predicts cis-regulatory modules based on perfect local ungapped sequences using comparative sequence data from multiple organisms.

::DEVELOPER

the Bergman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CisPlusFinder

:: MORE INFORMATION

Citation

Pierstorff, N., C.M. Bergman & T. Wiehe. (2006)
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.
Bioinformatics 22:2858-2864.

InferPPI 1.0 – Predict Protein Interactions based on Parsimony Tendency of Domain Interactions

InferPPI 1.0

:: DESCRIPTION

InferPPI aims to infer protein-protein interaction based on the parsimony principle of domain-domain interactions. Specifically, inferring domain interactions is a first step and formulated as an integer linear programming with different searching degree of training protein interaction. Then the model is solved by relaxed linear programming. By using the obtained domain interactions, novel protein interactions can be predicted by a formula. In contrast to probabilistic algorithms, InferPPI is an algorithm based on a deterministic model.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

   InferPPI

:: MORE INFORMATION

Citation

Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yong Wang, Shihua Zhang, Luonan Chen.
Predicting protein interactions based on parsimony tendency of domain interactions.
Manuscript, 2006.

Ampred – Predict the Antimicrobial Activity of given Sequence

Ampred

:: DESCRIPTION

Ampred server predicts the Antimicrobial activity of given sequence. The activity may be antifungal, antiviral and antibacterial .This server works based on Multidimensional signatures of antimicrobial peptides

::DEVELOPER

Leonsoji.T

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 no (only web service)

:: MORE INFORMATION

MeDor 1.4 – Metaserver for Predicting Protein Disorder

MeDor 1.4

:: DESCRIPTION

MeDor (Metaserver of Disorder) helps to identify protein disorder by providing a graphical interface with a unified view of the output of multiple disorder predictors. It allows fast, simultaneous analysis of a query sequence by multiple predictors and easy comparison of the prediction results. It also enables a standardized access to disorder predictors and allows meaningful comparisons among various query sequences.

::DEVELOPER

Sonia LONGHI

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  MeDor

:: MORE INFORMATION

Citation

“MeDor: a metaserver for predicting protein disorder.”
Philippe Lieutaud, Bruno Canard and Sonia Longhi.
BMC Genomics. 2008 Sep 16;9 Suppl 2:S25.PMID:18831791

Core 0.10 – Predict Protein Complex from PPI network

Core 0.10

:: DESCRIPTION

Core is an open source program for predicting protein complex from PPI network.

::DEVELOPER

Bioinformatics Research Group of Hong Kong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Core

:: MORE INFORMATION

Citation:

Predicting protein complexes from PPI data: a core-attachment approach.
Leung HC, Xiang Q, Yiu SM, Chin FY.
J Comput Biol. 2009 Feb;16(2):133-44.

 

SNAP – Predicts Effect of Mutations on Protein Function

SNAP

:: DESCRIPTION

SNAP (screening for non-acceptable polymorphisms) is a method for evaluating effects of single amino acid substitutions on protein function.SNAP identifies over 80% of the non-neutral mutations at 77% accuracy and over 76% of the neutral mutations at 80% accuracy at its default threshold. Each prediction is associated with a reliability index that correlates with accuracy and thereby enables experimentalists to zoom into the most promising predictions.

::DEVELOPER

Yana Bromberg in Rost Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 available upon request.

:: MORE INFORMATION

Citation

SNAP predicts effect of mutations on protein function.
Bromberg Y, Yachdav G, Rost B.
Bioinformatics. 2008 Oct 15;24(20):2397-8. Epub 2008 Aug 30.

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