eLSA 1.0.2 – Finding Time-Dependent Associations in Time Series Datasets

eLSA 1.0.2

:: DESCRIPTION

eLSA (Extended local similarity analysis) is a software of Finding Time-Dependent Associations in Time Series Datasets.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 eLSA

:: MORE INFORMATION

Citation

Li C Xia, Joshua A Steele, Jacob A Cram, Zoe G Cardon, Sheri L Simmons, Joseph J Vallino, Jed A Fuhrman and Fengzhu Sun
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
BMC Systems Biology 2011, 5(Suppl 2):S15

Quansong Ruan, Debojyoti Dutta, Michael S. Schwalbach, Joshua A. Steele, Jed A. Fuhrman, Fengzhu Sun (2006),
Local Similarity Analysis Reveals Unique Associations Among Marine Bacterioplankton Species and Environmental Factors.
Bioinformatics (2006) 22 (20): 2532-2538.

HMMEditor 1.2 – Visual Editor for Profile Hidden Markov Model

HMMEditor 1.2

:: DESCRIPTION

HMMEditor (HMMVE) is a visual editor for profile Hidden Markov Model (pHMM)

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

 HMMEditor

:: MORE INFORMATION

Citation

J. Dai and J. Cheng.
HMMEditor: A Visual Editing Tool for Profile Hidden Markov Model.
BMC Genomics. 9(S1):S8, 2008.

FastTree 2.1.11 – Cmpute Large Minimum Evolution Trees with Profiles

FastTree 2.1.11

:: DESCRIPTION

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

::DEVELOPER

by Morgan N. Price in Adam Arkin’s group at Lawrence Berkeley National Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

FastTree

:: MORE INFORMATION

Citation

Price, M.N., Dehal, P.S., and Arkin, A.P. (2009)
FastTree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix.
Molecular Biology and Evolution 26:1641-1650, doi:10.1093/molbev/msp077.

Price, M.N., Dehal, P.S., and Arkin, A.P. (2010)
FastTree 2 — Approximately Maximum-Likelihood Trees for Large Alignments.
PLoS ONE, 5(3):e9490. doi:10.1371/journal.pone.0009490.

eProS – Analysis of Protein Energy Profiles

eProS

:: DESCRIPTION

eProS is a database and toolbox for calculation, analysis, comparison and prediction of protein energy profiles

::DEVELOPER

BioInformatics Group Mittweida

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

eProS–a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles.
Heinke F, Schildbach S, Stockmann D, Labudde D.
Nucleic Acids Res. 2013 Jan;41(Database issue):D320-6. doi: 10.1093/nar/gks1079.

mirTarVis – Analysis tool for microRNA-mRNA Expression Profile data

mirTarVis

:: DESCRIPTION

miRTarVIs is a visual analysis tool for miRNA-mRNA expression profile data.

::DEVELOPER

Daekyoung Jung

:: SCREENSHOTS

miRTarVIs

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 miRTarVIs

:: MORE INFORMATION

Citation:

miRTarVis: an interactive visual analysis tool for microRNA-mRNA expression profile data.
Jung D, Kim B, Freishtat RJ, Giri M, Hoffman E, Seo J.
BMC Proc. 2015 Aug 13;9(Suppl 6 Proceedings of the 5th Symposium on Biological Data):S2. doi: 10.1186/1753-6561-9-S6-S2. eCollection 2015.

ORION – Profile-profile Fold Recognition

ORION

:: DESCRIPTION

ORION (Optimized fold RecognitION) is a new fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ORION

:: MORE INFORMATION

Citation

Improving protein fold recognition with hybrid profiles combining sequence and structure evolution.
Ghouzam Y, Postic G, de Brevern AG, Gelly JC.
Bioinformatics. 2015 Aug 7. pii: btv462.

UPP – Ultra-large alignments using Phylogeny-aware Profiles

UPP

:: DESCRIPTION

UPP addresses the problem of alignment of very large datasets, potentially containing fragmentary data.

::DEVELOPER

Siavash Mirarab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Python

:: DOWNLOAD

 UPP

:: MORE INFORMATION

Citation

Ultra-large alignments using phylogeny-aware profiles.
Nguyen NP, Mirarab S, Kumar K, Warnow T.
Genome Biol. 2015 Jun 16;16(1):124.

SCUDO – Signature-based Clustering of Expression Profiles

SCUDO

:: DESCRIPTION

SCUDO (Signature-based ClUstering for DiagnOstic purposes) is a tool for clustering gene expression profiles for diagnostic purposes using a new type of rank-based signatures

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SCUDO: a tool for signature-based clustering of expression profiles.
Lauria M, Moyseos P, Priami C.
Nucleic Acids Res. 2015 May 9. pii: gkv449.

NGS-Trex – NGS TRanscriptome profile EXplorer

NGS-Trex

:: DESCRIPTION

NGS-Trex is an automatic system for the analysis of NGS-Seq data.

::DEVELOPER

NGS-Trex team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 7:S10. doi: 10.1186/1471-2105-14-S7-S10. Epub 2013 Apr 22.
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer.
Boria I1, Boatti L, Pesole G, Mignone F.

MiRNA Profiling 0.2.7 – Profile Content of miRNA Sequencing Run

MiRNA Profiling 0.2.7

:: DESCRIPTION

MiRNA Profiling is a software to profile the content of a miRNA sequencing run.Given a set of aligned reads in 1 or more .sam files, produce an annotated version of the .sam where each read is given an annotation based on its coordinate. Additional summary information about the content of each sample is also generated, including miRNA species and other genomic features found.

::DEVELOPER

Andy Chu

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MiRNA Profiling

:: MORE INFORMATION

Based on analysis software used in Morin et al.,
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells.
,
Genome Res. 2008.18: 610-621