Jane – Journal / Author Name Estimator

Jane

:: DESCRIPTION

Just enter the title and/or abstract of the paper in the box, and click on ‘Find journals’ or ‘Find authors’. Jane will then compare your document to millions of documents in Medline to find the best matching journals or authors.

::DEVELOPER

the Biosemantics Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Mar 1;24(5):727-8. doi: 10.1093/bioinformatics/btn006. Epub 2008 Jan 28.
Jane: suggesting journals, finding experts.
Schuemie MJ, Kors JA.

ALE 20130717 – Assembly Likelihood Estimator

ALE 20130717

:: DESCRIPTION

ALE is a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid discovery of errors and comparisons between similar assemblies.

::DEVELOPER

Scott Clark@Cornell University Center for Applied Mathematics, Rob Egan@Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • C Compiler
  • Python

:: DOWNLOAD

 ALE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):435-43. doi: 10.1093/bioinformatics/bts723. Epub 2013 Jan 9.
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.
Clark SC, Egan R, Frazier PI, Wang Z.

GCE 1.0 – Genomic Character Estimator

GCE 1.0

:: DESCRIPTION

GCE is a bayes model based method to estimate the genome size ,genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be used to design the sequencing strategy.

::DEVELOPER

Binghang Liu (liubinghang@genomics.cn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GCE

:: MORE INFORMATION

Citation

Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects
Binghang Liu, Yujian Shi, Jianying Yuan, Xuesong Hu, Hao Zhang, Nan Li, Zhenyu Li, Yanxiang Chen, Desheng Mu, Wei Fan
arXiv:1308.2012

F-Seq 1.84 – Feature Density Estimator for High-Throughput Sequence Tags

F-Seq 1.84

:: DESCRIPTION

F-Seq is a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

::DEVELOPER

Furey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

 F-Seq

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 1;24(21):2537-8. doi: 10.1093/bioinformatics/btn480. Epub 2008 Sep 10.
F-Seq: a feature density estimator for high-throughput sequence tags.
Boyle AP, Guinney J, Crawford GE, Furey TS.

GraPPLE – Graph Property based Predictor and Likelihood Estimator

GraPPLE

:: DESCRIPTION

Graphs are abstract representations of relationships between entities. Through a set of instructions, they are able to convert relationships into nodes and edges. GraPPLE (originally: The RNA sorting hat) leverages the information available from graph properties and the predictive power of support vector machines (SVMs) to classify potential RNA sequences as functional/non-functional and into 1 of 46 Rfam families. In short, GraPPLE predicts the potential function of an ncRNA sequence.

::DEVELOPER

MPIMP Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 May;37(9):e66. Epub 2009 Apr 1.
Identification and classification of ncRNA molecules using graph properties.
Childs L, Nikoloski Z, May P, Walther D.

RASER 2.0 – The RAte Shift EstimatoR

RASER 2.0

:: DESCRIPTION

RASER is a likelihood based method for testing and detecting site-specific evolutionary rate shifts.
Given a multiple sequence alignment (MSA) and a phylogenetic tree, the program determines:
(a) Whether or not site-specific rate shifts characterize the evolution of a protein, and
(b) If so, points to the specific sites and lineages in which these shifts have most likely occurred.

::DEVELOPER

 Osnat Penn & Adi Stern

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 RASER

:: MORE INFORMATION

Citation

Penn O, Stern A, Rubinstein ND, Dutheil J, Bacharach E, Galtier N., Pupko T. 2008.
Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes.
PLoS Computational Biology 4(11): e1000214.

EMOGEE 20070704 – Estimator for MOdels of Gene Expression Evolution

EMOGEE 20070704

:: DESCRIPTION

EMOGEE (Estimator for MOdels of Gene Expression Evolution) implements neutral models for evolution of gene expression to analyze or simulate microarray data.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EMOGEE

:: MORE INFORMATION

Citation:

M. Rosskopf (2007)
Development and Applications of Neutral Models for Evolution of Gene Expression,
Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf

MareyMap 1.0 – Recombination Rate Estimator

MareyMap 1.0

:: DESCRIPTION

MareyMap is a meiotic recombination rate estimation program. It is based on R and features a graphical interfcace in tcl/tk. MareyMap comes with an extensive dataset and several interpolation methods. The user may also use MareyMap with his own data.

::DEVELOPER

Clement Rezvoy

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MareyMap

:: MORE INFORMATION

Citation

Rezvoy, C., Charif, D., Gueguen, L., Marais, G.A.B. (2007)
MareyMap: A R-based tool with graphical interface for estimating recombination rate.
Bioinformatics 23: 2188-2189.”