MS-Cluster 20110327 – Clustering Millions of Tandem Mass Spectra

MS-Cluster 20110327

:: DESCRIPTION

MS-Cluster is a software of clustering of MS/MS spectra takes advantage of this redundancy by identifying multiple spectra of the same peptide and replacing them with a single representative spectrum. Analyzing only representative spectra results in significant speed-up of MS/MS database searches. The new version of MSCluster also supports the creation of spectral archives.

::DEVELOPER

Ari Frank , CCMS The Center for Computational Mass Spectrometry

:: REQUIREMENTS

Linux/windows
java

:: DOWNLOAD

MS-Cluster

:: MORE INFORMATION

Citation:

Clustering Millions of Tandem Mass Spectra.
Ari M. Frank, Nuno Bandeira, Zhouxin Shen, Stephen Tanner, Steven P. Briggs, Richard D. Smith and Pavel A. Pevzner.
To appear in J. of Proteome Research, 2007.

TRhist 1.0.1 – Tandem Repeat Profiler in Personal Genomes

TRhist 1.0.1

:: DESCRIPTION

TRhist is a tool for finding significat tandem repeats using short reads.

::DEVELOPER

Morishita Laboratory, the University of Tokyo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
JRE

:: DOWNLOAD

TRhist

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 15;30(6):815-22. doi: 10.1093/bioinformatics/btt647. Epub 2013 Nov 8.
Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing.
Doi K1, Monjo T, Hoang PH, Yoshimura J, Yurino H, Mitsui J, Ishiura H, Takahashi Y, Ichikawa Y, Goto J, Tsuji S, Morishita S.

TRAL 2.0 – Tandem Repeat Annotation Library

TRAL 2.0

:: DESCRIPTION

TRAL makes annotation of tandem repeats in amino acid and nucleic data simple. TRAL includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs; statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.

::DEVELOPER

TRAL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
Python

:: DOWNLOAD

TRAL

:: MORE INFORMATION

Citation

TRAL: Tandem repeat annotation library.
Schaper E, Korsunsky A, Messina A, Murri R, Pečerska J, Stockinger H, Zoller S, Xenarios I, Anisimova M.
Bioinformatics. 2015 May 18. pii: btv306.

DTscore – Fast and Accurate Distance Algorithm to Reconstruct Tandem Duplication Trees

DTscore

:: DESCRIPTION

DTscore is a distance based tamdem duplication tree reconstruction algorithm. It is based on a simple tandem duplication model, which assumes unequal recombination (crossover) as the only duplication mechanism. All it takes as input is a distance matrix between copies. In this matrix, the rows and columns need to be ordered in the same way as the copies are ordered on the locus. DTscore can be applied to relatively large datasets (more than a hundred copies). Distances can be calculated using programs such as DNADIST (nucleotide sequences) or PROTDIST (protein sequences) from the PHYLIP package. Heterogeneous rates of substitution among sites can be dealt with using the GAMMA method, for example.

::DEVELOPER

DTscore team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

DTscore

:: MORE INFORMATION

Citation

Elemento O. and Gascuel O.
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees.
Bioinformatics. 2002 18 :S92-S99.

SIRIUS 4.9.3 – Identification of Metabolites using single and Tandem Mass Spectrometry

Sirius 4.9.3

:: DESCRIPTION

Sirius ,(Sum formula Identification by Ranking Isotope patterns Using mass Spectrometry) a new java-based software framework for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry. Sirius² deduces molecular formulas of small compounds by ranking isotope patterns from mass spectra of high resolution. Sirius² further analyses the fragmentation pattern of a compound resulting in hypothetical fragmentation trees. It allows for automated and high-throughput analysis of small-compound MS data beyond elemental composition without requiring compound structures or a mass spectral database.

::DEVELOPER

Lehrstuhl Bioinformatik Jena

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

Sirius

:: MORE INFORMATION

Citation:

SIRIUS: decomposing isotope patterns for metabolite identification
Sebastian B?cker, Matthias C. Letzel, Zsuzsanna Lipták and Anton Pervukhin
Bioinformatics (2009) 25 (2): 218-224

Crux 4.0 – Tandem Mass Spectrometry Analysis

Crux 4.0

:: DESCRIPTION

Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra.

::DEVELOPER

Noble Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

Crux

:: MORE INFORMATION

Citation:

Crux: rapid open source protein tandem mass spectrometry analysis.
McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS.
J Proteome Res. 2014 Oct 3;13(10):4488-91. doi: 10.1021/pr500741y.

Genomon ITDetector – Detecting Internal Tandem Duplication from Genome Sequence data

Genomon ITDetector

:: DESCRIPTION

Genomon-ITDetector is a software package for internal tandem duplication detection from cancer genome sequencing data.

::DEVELOPER

Kenichi Chiba, Yuichi Shiraishi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Genomon-ITDetector

:: MORE INFORMATION

Citation

Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data.
Chiba K, Shiraishi Y, Nagata Y, Yoshida K, Imoto S, Ogawa S, Miyano S.
Bioinformatics. 2014 Sep 4. pii: btu593.

Barnacle 1.0.4 – Detecting and Characterizing Tandem Duplications and Fusions in Transcriptome Assembly

Barnacle 1.0.4

:: DESCRIPTION

Barnacle (Browsing Assembled RNA for Chimeras with Localized Evidence) is a pipeline for detecting and characterizing chimeric transcripts from long RNA sequences, such as those generated by de novo transcriptome assembly.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Barnacle

:: MORE INFORMATION

Citation

BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550.
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.
Swanson L et al.

TRDistiller – Tandem Repeats Detection

TRDistiller

:: DESCRIPTION

TRDistiller is a rapid filter that is based on the comparison of composition and order of short strings in the adjacent sequence motifs.

::DEVELOPER

BiSMM – Structural Bioinformatics and Molecular Modeling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX
Java

:: DOWNLOAD

TRDistiller

:: MORE INFORMATION

Citation

J Struct Biol. 2014 Jun;186(3):386-91. doi: 10.1016/j.jsb.2014.03.013. Epub 2014 Mar 26.
TRDistiller: a rapid filter for enrichment of sequence datasets with proteins containing tandem repeats.
Richard FD, Kajava AV

STAR – Search for Tandem Approximate Repeats

STAR

:: DESCRIPTION

The program STAR (Search for Tandem Approximate Repeats) searches for significant Approximate Tandem Repeats (ATR) of a given motif in a DNA sequence. For each region of the sequence that is similar to a tandem repeat of the input motif, STAR returns a description of the segment that it calls a “Zone”, and an optimal alignment of the zone with the best possible Exact Tandem Repeat. (Here, exact means perfect.) STAR optimally detects all such zones in the sequence.

::DEVELOPER

Olivier Delgrange , Eric Rivals

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX

:: DOWNLOAD

STAR

:: MORE INFORMATION

Citation

“STAR: an algorithm to Search for Tandem Approximate Repeats.”
Delgrange O. and Rivals E.
Bioinformatics. 2004 20(16):2812-2820.