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.

CoLoRMap – Correcting Long noisy Reads by Mapping short reads

CoLoRMap

:: DESCRIPTION

CoLoRMap is a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CoLoRMap 

:: MORE INFORMATION

Citation

Haghshenas E, Hach F, Sahinalp SC, Chauve C.
CoLoRMap: Correcting Long Reads by Mapping short reads.
Bioinformatics. 2016 Sep 1;32(17):i545-i551. doi: 10.1093/bioinformatics/btw463. PMID: 27587673.

NAM 1.7.3 – Nested Association Mapping Analysis

NAM 1.7.3

:: DESCRIPTION

NAM is an R package that allows user to take into account prior information regarding population stratification to relax the linkage phase assumption of current methods.

::DEVELOPER

Alencar Xavier <xaviera at purdue.edu>, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R

:: DOWNLOAD

 NAM

:: MORE INFORMATION

Citation

NAM: Association Studies in Multiple Populations.
Xavier A, Xu S, Muir WM, Rainey KM.
Bioinformatics. 2015 Aug 4. pii: btv448.

PhosphOrtholog – Cross-species Mapping of Orthologous Protein Post-translational Modification

PhosphOrtholog

:: DESCRIPTION

PhosphOrtholog is a tool to map post-translational modification sites on proteins orthologous across species

::DEVELOPER

PhosphOrtholog team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.
Chaudhuri R, Sadrieh A, Hoffman NJ, Parker BL, Humphrey SJ, St?ckli J, Hill AP, James DE, Yang JY.
BMC Genomics. 2015 Aug 19;16(1):617. doi: 10.1186/s12864-015-1820-x.

TASR 1.1 – Annotate Transposable Elements using siRNAs Mapping

TASR 1.1

:: DESCRIPTION

TASR (Transposon Annotation using Small RNAs) is a bioinformatic pipeline that can annotate Transposable elements using siRNAs mapping

::DEVELOPER

TASR team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 TASR

:: MORE INFORMATION

Citation

A new approach for annotation of transposable elements using small RNA mapping.
El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA.
Nucleic Acids Res. 2015 Jul 27;43(13):e84. doi: 10.1093/nar/gkv257.

ContextMap 2.7.9 – Context-based mapping of RNA-seq data

ContextMap 2.7.9

:: DESCRIPTION

ContextMap is a very accurate read mapping tool for data from RNA-seq experiments. It can be used to refine mappings provided by other tools or as a standalone program.

::DEVELOPER

Institute for Bioinformatics, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 ContextMap

:: MORE INFORMATION

Citation

ContextMap 2: fast and accurate context-based RNA-seq mapping.
Bonfert T, Kirner E, Csaba G, Zimmer R, Friedel CC.
BMC Bioinformatics. 2015 Apr 17;16(1):122. doi: 10.1186/s12859-015-0557-5.

Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel.
A context-based approach to identify the most likely mapping for RNA-seq experiments.
BMC Bioinformatics, vol 13(Suppl 6), pp. S9, 2012.

GenePainter 2.0.5 – Mapping Gene Structures onto Protein Multiple Sequence Alignment

GenePainter 2.0.5

:: DESCRIPTION

GenePainter is a standalone tool for mapping gene structures onto protein multiple sequence alignments (MSA). Gene structures, as provided by WebScipio, are aligned with respect to the exact positions of the introns (down to nucleotide level) and intron phase. Output can be viewed in various formats, ranging from plain text to graphical output formats.

::DEVELOPER

kollmar_group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Ruby

:: DOWNLOAD

  GenePainter

:: MORE INFORMATION

Citation

S. Mühlhausen, M. Hellkamp & M. Kollmar (2014)
GenePainter 2.0 resolves the taxonomic distribution of intron positions.
Bioinformatics, pii: btu798

Björn Hammesfahr †, Florian Odronitz †, Stefanie Mühlhausen, Stephan Waack & Martin Kollmar (2013)
GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures.
BMC Bioinformatics 14, 77.

BS Seeker 2.1.8 – Mapping of Bisulfite-treated Short Reads

BS Seeker 2.1.8

:: DESCRIPTION

BS Seeker (Bisulfite sequencing) performs accurate and fast mapping of bisulfite-treated short reads. It aligns Bisulfite-treated reads generated from the Cokus et al’s library protocol (with tags) or the Lister et al’s library protocol (with no tags).

::DEVELOPER

Matteo Pellegrini Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BS Seeker

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 Nov 10;14:774. doi: 10.1186/1471-2164-14-774.
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY1, Pellegrini M.

BMC Bioinformatics. 2010 Apr 23;11:203.
BS Seeker: precise mapping for bisulfite sequencing.
Chen PY, Cokus SJ, Pellegrini M.

SIRAH 2.2 – Mapping, Backmapping and Visualization of Coarse-grained Models

SIRAH 2.2

:: DESCRIPTION

SIRAH Tools (Southamerican Initiative for a Rapid and Accurate Hamiltonian) comprises a set of utilities to convert all-atoms coordinates to arbitrary residue-based CG schemes, write GROMACS’ topological information at any resolution into PSF format and a VMD plugin to visualize, analyze and retrieve pseudo-atomistic information from CG trajectories performed with the SIRAH force field.

::DEVELOPER

SIRAH team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • AMBER/ GROMACS

:: DOWNLOAD

 SIRAH

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Jan 14. pii: btw020.
SIRAH Tools: mapping, backmapping and visualization of coarse-grained models.
Machado M, Pantano S