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

Mauve 2.4.0 – Multiple Genome Alignments

Mauve 2.4.0

:: DESCRIPTION

Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics on a new scale. Aligning whole genomes is a fundamentally different problem than aligning short sequences.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours.

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 Mauve

:: MORE INFORMATION

Citation

Aaron C.E. Darling, Bob Mau, Frederick R. Blatter, and Nicole T. Perna. 2004.
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
Genome Research. 14(7):1394-1403.

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

PMFastR – New Approach to Multiple RNA Structure Alignment

PMFastR

:: DESCRIPTION

PMFastR is an algorithm which iteratively uses a sequence-structure alignment procedure to build a multiple RNA structure alignment

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PMFastR

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2011 Apr 29. [Epub ahead of print]
A Memory Efficient Method for Structure-Based RNA Multiple Alignment.
Deblasio D, Bruand J, Zhang S.

MIL – Multiple Instance Learning for Protein-DNA Interaction Modeling

MIL

:: DESCRIPTION

MIL(multiple-instance learning) is a novel algorithm, which breaks each DNA sequence into multiple overlapping subsequences and models each subsequence separately, therefore implicitly takes into consideration binding site locations, resulting in both higher accuracy and better interpretability of the models.

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  •  MatLab

:: DOWNLOAD

MIL

:: MORE INFORMATION

Citation

Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning.
Gao Z, Ruan J.
Bioinformatics. 2017 Jul 15;33(14):2097-2105. doi: 10.1093/bioinformatics/btx115.

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.

SARA-Coffee 1.0.7 – Accurate Multiple RNA Structural Alignment

SARA-Coffee 1.0.7

:: DESCRIPTION

SARA-Coffee is a structure based multiple RNA aligner. This is a new algorithm that joins the pairwise RNA structure alignments performed by SARA with the multiple sequence T-Coffee framework. SARA-Coffee is part of the T-Coffee distribution.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SARA-Coffee

:: MORE INFORMATION

Citation:

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.
Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P, Notredame C.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W356-60. doi: 10.1093/nar/gku459.

SMAT 0.98 – Scaled Multiple-phenotype Association Test

SMAT 0.98

:: DESCRIPTION

SMAT is an R package for performing the Scaled Multiple-phenotype Association Test in cohort or case-control designs to assess common effect of a single nucleotide polymorphism (SNP) on multiple (positively correlated) continuous outcomes measuring the same underlying trait.

::DEVELOPER

Xihong Lin’s Group, Harvard School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SMAT

:: MORE INFORMATION

Citation

Genome-wide Association Analysis for Multiple Continuous Secondary Phenotypes.
Schifano ED, Li L, Christiani DC, Lin X.
Am J Hum Genet. 2013 May 2;92(5):744-59.

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.