Tag: Multiple

PathoGiST v0.3.6 – Clustering Pathogen Isolates by combining multiple Genotyping Signals

PathoGiST v0.3.6

:: DESCRIPTION

PathOGiST is an algorithmic framework for clustering bacterial isolates by leveraging multiple genotypic signals and calibrated thresholds.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • conda

:: DOWNLOAD

PathOGiST

:: MORE INFORMATION

Citation

Katebi M. et al. (2020)
PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals.
Algorithms for Computational Biology. AlCoB 2020. Lecture Notes in Computer Science, vol 12099. Springer, Cham. https://doi.org/10.1007/978-3-030-42266-0_9

IntNMF 1.2.0 – Integrative Clustering of Multiple Genomic Dataset

IntNMF 1.2.0

:: DESCRIPTION

IntNMF is an R package for Integrative clustering of multiple genomic datasets with Non-negative matrix factorization (NMF).

::DEVELOPER

Fridley Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

IntNMF

:: MORE INFORMATION

Citation:

Chalise P, Fridley BL.
Integrative clustering of multi-level ‘omic data based on non-negative matrix factorization algorithm.
PLoS One. 2017 May 1;12(5):e0176278. doi: 10.1371/journal.pone.0176278. PMID: 28459819; PMCID: PMC5411077.

ProPIP – Progressive Multiple Sequence Alignment with Poisson Indel Process

ProPIP

:: DESCRIPTION

ProPIP is a Multiple Sequence Alignment inference software that implements the Poisson Indel Process (Bouchard-Côté & Jordan, PNAS, 2013) in the Maximum Likelihood framework.

::DEVELOPER

Applied Computational Genomics Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ProPIP

:: MORE INFORMATION

Citation

Maiolo M, Gatti L, Frei D, Leidi T, Gil M, Anisimova M.
ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process.
BMC Bioinformatics. 2021 Oct 24;22(1):518. doi: 10.1186/s12859-021-04442-8. PMID: 34689750; PMCID: PMC8543915.

TMT-Integrator 1.0.8 – Extract and Combine Channel Abundances from multiple TMT samples

TMT-Integrator 1.0.8

:: DESCRIPTION

TMT-Integrator is a tool that integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Java

:: DOWNLOAD

TMT-Integrator 

:: MORE INFORMATION

ModView 0.903 – Visualization of Multiple Protein Sequences & Structures

ModView 0.903

:: DESCRIPTION

ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. As a Netscape plug-in , it can be embed into Web pages and controlled by JavaScript objects on the page. It has wide range of tools to manipulate and analyze sequences and structures by interactive control.

::DEVELOPER

Andrej Sali

:: SCREENSHOTS

:: REQUIREMENTS

  • Netscape 4.xx

:: DOWNLOAD

ModView

:: MORE INFORMATION

Citation:

Bioinformatics. 2003 Jan;19(1):165-6.
ModView, visualization of multiple protein sequences and structures.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A.

HAlign 2.1 – Fast Multiple Similar DNA/RNA Sequence Alignment

HAlign 2.1

:: DESCRIPTION

HAlign is a package of multi-platform Java software tools, which aimed at large scale multiple similar DNA/RNA sequence alignment. HAlign employs center star multiple sequence alignment strategy.

::DEVELOPER

Dr. Quan Zou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JRE
  • Hadoop

:: DOWNLOAD

 HAlign

:: MORE INFORMATION

Citation

HAlign: Fast Multiple Similar DNA/RNA Sequence Alignment Based on the Centre Star Strategy.
Zou Q, Hu Q, Guo M, Wang G.
Bioinformatics. 2015 Mar 25. pii: btv177.

MulPBA – Multiple Protein Structure Alignment

MulPBA

:: DESCRIPTION

mulPBA is an efficient tool for comparison of protein structures based on similarity in the local backbone conformation.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.
Léonard S, Joseph AP, Srinivasan N, Gelly JC, de Brevern AG.
J Biomol Struct Dyn. 2014 Apr;32(4):661-8. doi: 10.1080/07391102.2013.787026.

MEAP 2.0.2 – Multiple Exon Array Preprocessing

MEAP 2.0.2

:: DESCRIPTION

MEAP is an R package for large-scale exon array data analysis.It includes a novel algorithm (PM-BayesBG) to estimate sequence-based backgrounds that allows more reliable expression estimation than the existing background correction methods. MEAP also contains algorithms for generating robust expression estimates at exon, alternatively spliced variant and gene levels that facilitates the quantitative analysis of alternative spliced variants in the whole transcriptome.

::DEVELOPER

Hautaniemi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R Package

:: DOWNLOAD

 MEAP

:: MORE INFORMATION

Citation

Chen P, Lepikhova T, Hu YZ, Monni O and Hautaniemi S.
Comprehensive Exon Array Data Processing Method for Quantitative Analysis of Alternative Spliced Variants.
Nucleic Acids Research. 2011 Oct;39(18):e123. Epub 2011 Jul 10.

mGPfusion – Predicting Stability Changes upon Single and Multiple Mutations

mGPfusion

:: DESCRIPTION

mGPfusion is a Gaussian process based method for predicting stability changes upon single and multiple mutations of proteins that complements the available experimental data with large amounts of simulated data.

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

mGPfusion

:: MORE INFORMATION

Citation

Bioinformatics, 34 (13), i274-i283 2018 Jul 1
mGPfusion: Predicting Protein Stability Changes With Gaussian Process Kernel Learning and Data Fusion
Emmi Jokinen , Markus Heinonen , Harri Lähdesmäki

Exit mobile version