HECTOR 1.0 – A Parallel Homopolymer Spectrum based 454 Error Corrector

HECTOR 1.0

:: DESCRIPTION

HECTOR is a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. In this algorithm, for the first time we have investigated a novel homopolymer spectrum based approach to handle homopolymer insertions or deletions, which are the dominant sequencing errors in 454 short-reads.

::DEVELOPER

HECTOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

HECTOR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 6;15(1):131. [Epub ahead of print]
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data.
Wirawan A, Harris RS, Liu Y, Schmidt B, Schröder J.

specL 1.26.0 – Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

specL 1.26.0

:: DESCRIPTION

specL provides a function for generating spectra libraries which can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software.

::DEVELOPER

specL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux /MacOsX
R/Bioconductor

:: DOWNLOAD

specL

:: MORE INFORMATION

Citation:

specL – An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics.
Panse C, Trachsel C, Grossmann J, Schlapbach R.
Bioinformatics. 2015 Feb 23. pii: btv105.

SFselect – Learning Natural Selection from the Site Frequency Spectrum

SFselect

:: DESCRIPTION

SFselect is a method for classifying genomic regions evolving under positive selection, from those evolving neutrally

::DEVELOPER

Roy Ronen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SFselect

:: MORE INFORMATION

Citation

Genetics. 2013 Sep;195(1):181-93. doi: 10.1534/genetics.113.152587. Epub 2013 Jun 14.
Learning natural selection from the site frequency spectrum.
Ronen R, Udpa N, Halperin E, Bafna V.

SRF 1.1 – Find Repeats through an analysis of the power Spectrum of a given DNA Sequence

SRF 1.1

:: DESCRIPTION

SRF (Spectral Repeat Finder) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. SRF is an ab initio technique as no prior assumptions need to be made regarding either the repeat length, its fidelity, or whether the repeats are in tandem or not

::DEVELOPER

SRF Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Jun 12;20(9):1405-12. Epub 2004 Feb 19.
Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.
Sharma D, Issac B, Raghava GP, Ramaswamy R.

oncSpectrum 1.0 – Likelihood Analysis of the Spectrum of Somatic Mutations in Cancers

oncSpectrum 1.0

:: DESCRIPTION

oncSpectrum : Likelihood Analysis of the Spectrum of Somatic Mutations in Cancers
::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows
C Compiler

:: DOWNLOAD

oncSpectrum

:: MORE INFORMATION

Citation

Z. Yang, S. Ro and B. Rannala. 2003.
Likelihood models of somatic mutation and codon substitution in cancer genes.
Genetics 165: 695-705.

Spectrum 2.0 – Show Phylogenetic Information in a Data Set

Spectrum 2.0

:: DESCRIPTION

Spectrum is a program designed to read in a data file comprising aligned character arrays (such as DNA sequence data) or distance data in the form of a matrix, and perform some simple spectral analysis procedures on that data.The input file format is NEXUS, as used in PAUP and MacClade.The program reads in phylogenetic 4-state or binary data, or distance data, and outputs the bipartition spectra corresponding to the data. It can also be used it to find the tree whose expected spectrum is closest to your observed spectrum (the “closest tree” and “Manhattan tree”– see the manual). Spectrum outputs spectra in Excel format as tab-delimited text files and trees as TreeView files.

::DEVELOPER

Dr. Michael Charleston

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Macintosh

:: DOWNLOAD

Spectrum

:: MORE INFORMATION

Please register your copy of Spectrum! It costs nothing, and if you register I can keep you up to date with bugs, bug fixes, updates etc. E-mail me to register.