Crux 2.1 – Tandem Mass Spectrometry Analysis

Crux 2.1

:: 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.

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

SIRIUS 3.0.3 – Identification of Metabolites using single and Tandem Mass Spectrometry

 Sirius 3.0.3

:: 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

SIRIUS

:: 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

ProRepeat – An Integrated Repository for studying Amino Acid Tandem Repeats in Proteins

ProRepeat

:: DESCRIPTION

ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats.

::DEVELOPER

ProRepeat team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jan;40(Database issue):D394-9. doi: 10.1093/nar/gkr1019. Epub 2011 Nov 18.
ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins.
Luo H1, Lin K, David A, Nijveen H, Leunissen JA.

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.

Barnacle 1.0.3 – Detecting and Characterizing Tandem Duplications and Fusions in Transcriptome Assembly

Barnacle 1.0.3

:: 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.

TRAL 0.3.5 – Tandem Repeat Annotation Library

TRAL 0.3.5

:: 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.

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.

ADEPTS – Advanced Peptide De Novo Sequencing with a Pair of Tandem Mass Spectra

ADEPTS

:: DESCRIPTION

ADEPTS is a software package for peptide identification using two different types of MS/MS spectra.

::DEVELOPER

Lin He

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

  ADEPTS

:: MORE INFORMATION

Citation

ADEPTS: advanced peptide de novo sequencing with a pair of tandem mass spectra.
He L, Ma B.
J Bioinform Comput Biol. 2010 Dec;8(6):981-94.

GlycoMaster DB – Assist the automated Identification of N-linked Glycopeptides by Tandem Mass Spectrometry

GlycoMaster DB

:: DESCRIPTION

GlycoMaster DB is a MS-based intact glycopeptide identification software tool, which simultaneously identifies the glycopeptide sequence and the attached glycan moiety.

::DEVELOPER

Lin He

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Proteome Res. 2014 Sep 5;13(9):3881-95. doi: 10.1021/pr401115y. Epub 2014 Aug 25.
GlycoMaster DB: software to assist the automated identification of N-linked glycopeptides by tandem mass spectrometry.
He L1, Xin L, Shan B, Lajoie GA, Ma B.