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.

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.

txCoords – Mapping and Extending Genomic Coordinates to Transcripts

txCoords

:: DESCRIPTION

txCoords is a novel and easy-to-use web application for transcriptomic peak re-mapping.

::DEVELOPER

Sun Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

txCoords: A Novel Web Application for Transcriptomic Peak Re-mapping.
Yan Z, Liu K, Xiang S, Sun Z.
IEEE/ACM Trans Comput Biol Bioinform. 2016 May 16.

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.

Hobbes 3.0 – Genome Sequence Mapping

Hobbes 3.0

:: DESCRIPTION

Hobbes is a software package for efficiently mapping DNA snippets (reads) against a reference DNA sequence. It can map short and long reads, and supports Hamming distance (only substitutions) and edit distance (substitutions/insertions/deletions). Hobbes accepts both single-end and paired-end reads for alignment, and can run on multiple CPU cores using multithreading.

::DEVELOPER

Hobbes Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Hobbes

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Feb 5;15:42. doi: 10.1186/1471-2105-15-42.
Improving read mapping using additional prefix grams.
Kim J, Li C, Xie X

Nucleic Acids Res. 2012 Mar;40(6):e41. doi: 10.1093/nar/gkr1246. Epub 2011 Dec 22.
Hobbes: optimized gram-based methods for efficient read alignment.
Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X.

SeqTrimMap 1.0 – Sequential Trimming and Mapping of Short Reads

SeqTrimMap 1.0

:: DESCRIPTION

SeqTrimMap is a script for efficient mapping of short reads from high-thoughput sequencing experiments.

::DEVELOPER

SGJlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SeqTrimMap

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):318-23. doi: 10.1093/bioinformatics/btr686
Detection of microRNAs in color space.
Marco A, Griffiths-Jones S.

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

SIRAH

:: 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

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

SPALN 2.2.1 – Mapping and Alignment of a set of cDNA Sequences onto a Genomic Sequence

SPALN 2.2.1

:: 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.

SPALN Online Version

::DEVELOPER

Osamu Gotoh

:: 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).

GenePainter 2.0.3 – Mapping Gene Structures onto Protein Multiple Sequence Alignment

GenePainter 2.0.3

:: 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

motorprotein

:: 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.