MARIO 0.4 – Mapping RNA-RNA interactome and RNA Structure

MARIO 0.4

:: DESCRIPTION

MARIO (Mapping RNA-RNA interactome in vivo) is a tools to study RNA-RNA interactome and structures in vivo.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BioPython

:: DOWNLOAD

MARIO

:: MORE INFORMATION

Citation

Nat Commun. 2016 Jun 24;7:12023. doi: 10.1038/ncomms12023.
Mapping RNA-RNA interactome and RNA structure in vivo by MARIO.
Nguyen TC, Cao X, Yu P, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S.

WMap 20091230 – Mapping of Sequence Reads

WMap 20091230

:: DESCRIPTION

WMap is a new sequence mapping software designed to map high-throughput sequencing reads as well as methylated-C reads, enabling usage of such sequencing data to various fields of biological research.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 WMap

:: MORE INFORMATION

Infomap Bioregions – Interactive mapping of Biogeographical Regions from Species Distributions

Infomap Bioregions

:: DESCRIPTION

Infomap Bioregions is an interactive web application that inputs species distribution data and generates bioregion maps.

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Syst Biol. 2017 Mar 1;66(2):197-204. doi: 10.1093/sysbio/syw087.
Infomap Bioregions: Interactive Mapping of Biogeographical Regions from Species Distributions.
Edler D, Guedes T, Zizka A, Rosvall M, Antonelli A

Algpred – Prediction of Allergenic Proteins and mapping of IgE Epitopes

Algpred

:: DESCRIPTION

AlgPred is a web server which has been developed for the predicting allergenic proteins and for mapping IgE epitopes on allergenic proteins

::DEVELOPER

Algpred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W202-9.
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes.
Saha S1, Raghava GP.

SPALN 2.3.3f – Mapping and Alignment of a set of cDNA Sequences onto a Genomic Sequence

SPALN 2.3.3f

:: DESCRIPTION

Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. Spaln adopts multi-phase heuristics that makes it possible to perform the job on a conventional personal computer running under Unix/Linux with limited memory. The program is written in C++ and distributed as source codes and also as executables for a few platforms. Unless binaries are not provided, users must compile the program on their own system. Although the program has been tested only on a Linux operating system, it is likely to be portable to most Unix systems with little or no modifications. The accessory program sortgrcd sorts the gene loci found by spaln in the order of chromosomal position and orientation.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 SPALN

:: MORE INFORMATION

Citation

Gotoh, O.
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence
Nucleic Acids Research 36 (8) 2630-2638 (2008).

MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments

MIMEAnTo

:: DESCRIPTION

Quantitative effects of each mutation at each position in the RNA can be recovered with statistical certainty using the herein developed user-friendly, cross-platform software MIMEAnTo (MIME Analysis Tool).

::DEVELOPER

MIMEAnTo team

:: SCREENSHOTS

MIMEAnTo

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Gnuplot

:: DOWNLOAD

 MIMEAnTo

:: MORE INFORMATION

Citation:

MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments.
Smith MR, Smyth RP, Marquet R, von Kleist M.
Bioinformatics. 2016 Jul 10. pii: btw479.

SeqSaw 1.0.8 – Short Spliced Sequence Mapping Tool

SeqSaw 1.0.8

:: DESCRIPTION

SeqSaw is a package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

::DEVELOPER

SeqSaw team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SeqSaw

:: MORE INFORMATION

Citation

Biochem Biophys Res Commun. 2011 Jun 3;409(2):299-303. Epub 2011 May 7.
Observations on novel splice junctions from RNA sequencing data.
Wang L, Wang X, Wang X, Liang Y, Zhang X.

<

SNPAAMapper 2.0 – A SNP Amino Acid Mapping tool

SNPAAMapper 2.0

:: DESCRIPTION

SNPAAMapper is a downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5’UTR, etc).

::DEVELOPER

Computational Biology Lab at Indiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PErl

:: DOWNLOAD

  SNPAAMapper

:: MORE INFORMATION

Citation

Bioinformation. 2013 Oct 16;9(17):870-2. doi: 10.6026/97320630009870. eCollection 2013.
SNPAAMapper: An efficient genome-wide SNP variant analysis pipeline for next-generation sequencing data.
Bai Y1, Cavalcoli J.

RazerS 3.5.4 – Fast Read Mapping with Sensitivity Control

RazerS 3.5.4

:: DESCRIPTION

RazerS is a tool for mapping millions of short genomic reads onto a reference genome. It was designed with focus on mapping next-generation sequencing reads onto whole DNA genomes. RazerS searches for matches of reads with a percent identity above a given threshold, whereby it detects matches with mismatches as well as gaps.

RazerS uses a k-mer index of all reads and counts common k-mers of reads and the reference genome in parallelograms. Each parallelogram with a k-mer count above a certain threshold triggers a verification. On success, the genomic subsequence and the read number are stored and written to the output file.

::DEVELOPER

David Weese

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows

:: DOWNLOAD

RazerS

:: MORE INFORMATION

Citation

RazerS – Fast Read Mapping with Sensitivity Control
David Weese, Anne-Katrin Emde, Tobias Rausch, Andreas Döring, and Knut Reinert
Genome Research, Sep 2009, 19: pp. 1646-1654

Bioinformatics. 2012 Oct 15;28(20):2592-9. doi: 10.1093/bioinformatics/bts505.
RazerS 3: faster, fully sensitive read mapping.
Weese D, Holtgrewe M, Reinert K.

geQTL – Unraveling Group and individual Associations in eQTL Mapping

geQTL

:: DESCRIPTION

geQTL is a sparse regression method that can detect both group-wise and individual associations between SNPs and expression traits.

::DEVELOPER

Wei Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler / MatLab

:: DOWNLOAD

 geQTL

:: MORE INFORMATION

Citation

Sparse regression models for unraveling group and individual associations in eQTL mapping.
Cheng W, Shi Y, Zhang X, Wang W.
BMC Bioinformatics. 2016 Mar 22;17(1):136. doi: 10.1186/s12859-016-0986-9.