MicroRazerS 1.0 – Rapid Alignment of small RNA reads

MicroRazerS 1.0

:: DESCRIPTION

MicroRazerS is a tool optimized for mapping small RNAs onto a reference genome. It is an order of magnitude faster than Mega BLAST and comparable in speed with other short read mapping tools. In addition, it is more sensitive and easy to handle and adjust.

::DEVELOPER

Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert and Silke Sperling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MicroRazerS

:: MORE INFORMATION

Citation

Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert and Silke Sperling.
MicroRazerS: rapid alignment of small RNA reads.
Bioinformatics (2010) 26 (1): 123-124

DySC 20120601 – Software for Greedy Clustering of 16S rRNA Reads

DySC 20120601

:: DESCRIPTION

DySC is a new tool based on the greedy clustering approach which uses a dynamic seeding strategy. Evaluations based on the normalized mutual information criterion shows that DySC produces higher quality clusters than UCLUST and CD-Hit at a comparable runtime.

::DEVELOPER

Zejun Zheng, Stefan Kramer and Bertil Schmidt

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

DySC

:: MORE INFORMATION

Citation

DySC: software for greedy clustering of 16S rRNA reads.
Zheng Z, Kramer S, Schmidt B.
Bioinformatics. 2012 Aug 15;28(16):2182-3. Epub 2012 Jun 23.

STAR 1.0 – Significance Tester for the Accumulation of Reads

STAR 1.0

:: DESCRIPTION

STAR identify regions enriched for a histone modification based on ChIP-Seq evidence, by identifying regions with a significant accumulation of reads.

::DEVELOPER

STAR Team

:: REQUIREMENTS

Windows/Mac OsX/ Linux
JAVA

:: DOWNLOAD

STAR

:: MORE INFORMATION

Hybrid SHREC – Error Correction Algorithm for Correcting Reads

Hybrid SHREC

:: DESCRIPTION

Hybrid SHREC is an error correction algorithm for correcting reads from various DNA sequencing platforms. We provide two versions of the algorithm: one that performs the error correction in base space and is limited to normal base space reads and another that performs error correction in the color space of the SOLiD sequencing technology by Applied Biosystems.

::DEVELOPER

Leena Salmela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Hybrid SHREC

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 May 15;26(10):1284-90. Epub 2010 Apr 8.
Correction of sequencing errors in a mixed set of reads.
Salmela L.

SEQIO 1.2.2 – Read and Write Biological Sequence Files

SEQIO 1.2.2

:: DESCRIPTION

The SEQIO package is a set of C functions which can read and write biological sequence files formatted using various file formats and which can be used to perform database searches on biological databases.

::DEVELOPER

Dan Gusfield’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
C Compiler

:: DOWNLOAD

SEQIO

:: MORE INFORMATION

Readseq 2.1.30 – Read & Reformat Biosequences

Readseq 2.1.30

:: DESCRIPTION

ReadSeq is a biosequence data translator. It’s main contribution to bioinformatics is it takes on the job of guessing what your input biosequence data format is, and converting it to what your software knows how to handle.

::DEVELOPER

Don Gilbert at Indiana University

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

Readseq

:: MORE INFORMATION

Anyone can use Readseq. There are no copyright restrictions, it is in the PUBLIC DOMAIN.

Dangle 0.63 – Read PDB File & Generate Geometric Measurement Table

Dangle 0.63

:: DESCRIPTION

Dangle an updated and more general version of our program Dang in that it reads coordinates from a Protein DataBank (PDB) coordinate file for either protein or nucleic acid and generates geometric measurements for each residue. It is different from Dang in that Dangle: is Java-based, includes the capability of reporting deviations from ideal geometry as well as measurement values, and has a very flexible input syntax for specified the measurements desired. Dangle output is given as colon-delimited values, one line per residue. It is designed for facile use in scripts, and is the usual source of input for Suitename, either to generate the data for MolProbity’s multi-criterion table or in individual command-line use.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Java

:: DOWNLOAD

Dangle

:: MORE INFORMATION

Dangle is free software available under the terms of its own BSD-style license.

Dang 1.8 – Read PDB File & Generate Geometric Measurement Table

Dang 1.8

:: DESCRIPTION

Dang reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base. In its most basic form, it writes out dihedral angles (phi, psi, chi) hence the name. The output is formated for easy parsing by awk, grep, sort and other UNIX utilities.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Linux/Mac OsX/SGI-irix/Sun-SPARC

:: DOWNLOAD

Dang

:: MORE INFORMATION

Dang is free software available under the terms of its own BSD-style license.