SARA-Coffee – Accurate Multiple RNA Structural Alignment

SARA-Coffee

:: 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.

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

Genome Evolution Laboratory

:: 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.

DynMap 0.0.20 – Mapping Short Reads to Multiple related Genomes

DynMap 0.0.20

:: DESCRIPTION

DynMap is an efficient, accurate, and sensitive tool for aligning short reads, obtained from next-generation sequencing, to multiple closely-related genomes. The programme can handle an enormous amount of single-end reads generated by the next-generation Illumina/Solexa Genome Analyzer.

:: DEVELOPER

Dr. Solon P. Pissis

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  •  Linux
  • C Compiler

:: DOWNLOAD

 DynMap

:: MORE INFORMATION

Citation

Tomas Flouri, Costas S. Iliopoulos, and Solon P. Pissis.
DynMap : mapping short reads to multiple related genomes.
In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), pp. 330-334, 2011. ACM Digital Library

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.

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.

HAlign 1.1 – Fast Multiple Similar DNA/RNA Sequence Alignment

HAlign 1.1

:: 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.

BAMSE – Bayesian Association for Multiple SNP Effects

BAMSE

:: DESCRIPTION

BAMSE is a software for performing association studies of multiple SNPs and environmental factors.

::DEVELOPER

BAMSE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

 BAMSE

:: 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.

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.