TopPIC 1.5 – TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization

TopPIC 1.5

:: DESCRIPTION

TopPIC is a software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search.

::DEVELOPER

TopPIC team

:: REQUIREMENTS

  • Linux/windows

:: DOWNLOAD

 TopPIC

:: MORE INFORMATION

Citation:

TopPIC: A software tool for top-down mass spectrometry-based proteoform identification and characterization.
Kou Q, Xun L, Liu X.
Bioinformatics. 2016 Jul 16. pii: btw398.

Protein identification using top-down spectra.
Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA.
Mol Cell Proteomics. 2012 Jun;11(6):M111.008524. doi: 10.1074/mcp.M111.008524.

TERA-Seq – True end-to-end Sequencing of native RNA molecules for Transcriptome Characterization

TERA-Seq

:: DESCRIPTION

TERA-Seq (True End-to-end RNA Sequencing) is a platform that addresses these limitations, permitting more thorough transcriptome characterization.

::DEVELOPER

Z. MOURELATOS LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TERA-Seq

:: MORE INFORMATION

Citation

Ibrahim F, Oppelt J, Maragkakis M, Mourelatos Z.
TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization.
Nucleic Acids Res. 2021 Aug 24:gkab713. doi: 10.1093/nar/gkab713. Epub ahead of print. PMID: 34428294.

FCMM 2.0.0 – Functional Characterization of Multiple Metagenome samples

FCMM 2.0.0

:: DESCRIPTION

FCMM is a pipeline for top-k based functional characterization of multiple metagenome samples to infer the major functions as well as their quantitative scores in a comparative metagenomics manner.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • awk (GNU awk 3.1.7)
  • sed (GNU sed 4.2.1)
  • BWA (v0.7.10)
  • DIAMOND (v0.7.8.57)
  • Trimmomatic (v0.33)

:: DOWNLOAD

 FCMM

:: MORE INFORMATION

Citation

FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples.
Lee J, Lee HT, Hong WY, Jang E, Kim J.
J Microbiol Methods. 2015 Aug;115:121-8. doi: 10.1016/j.mimet.2015.05.023

CSZ 1.0 – Characterization of small RNAome for Zebrafish

CSZ 1.0

:: DESCRIPTION

CSZ demonstrats an sRNA class transition from piRNAs to miRNAs as development proceeds.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CSZ

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Feb 10;15:117. doi: 10.1186/1471-2164-15-117.
Systematic characterization of small RNAome during zebrafish early developmental stages.
Yao Y, Ma L, Jia Q, Deng W, Liu Z, Zhang Y, Ren J, Xue Y, Jia H1, Yang Q.

EpIC – Epitope Immunogenicity Characterization

EpIC

:: DESCRIPTION

EpIC is a software program that is designed to enable optimization of peptide epitopes for vaccine applications. Peptide-based vaccines offer many advantages over traditional vaccine platforms in terms of cost, safety, and ease of production.

::DEVELOPER

Bioinformatics Research Group, University of Saskatchewan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

EpIC: A Rational Pipeline for Epitope Immunogenicity Characterization.
Marciniuk K, Trost B, Napper S.
Bioinformatics. 2015 Mar 6. pii: btv136

MOLE 2.5 – Location and Characterization of Channels, Tunnels and Pores in Molecular Structures

MOLE 2.5

:: DESCRIPTION

Program MOLE is an universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in molecular structures. The core of MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. MOLE is a powerful software (overcomming some limitations of CAVER tool) for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories (AMBER ascii traj and parm7 are supported) in which analysis of a large number of snapshots is required.

::DEVELOPER

Martin Petrek (NCBR), Michal Otyepka (FCH UPOL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

MOLE

:: MORE INFORMATION

Citation:

Structure. 2007 Nov;15(11):1357-63.
MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.
Petrek M, Kosinová P, Koca J, Otyepka M.

FUCHS 0.3.0 – FUll circular RNA CHaracterization from RNA-Seq

FUCHS 0.3.0

:: DESCRIPTION

FUCHS is a python pipeline designed to fully characterize circular RNAs. It uses a list of circular RNAs and reads spanning the back-splice junction as well as a BAM file containing the mapping of all reads (alternatively of all chimeric reads).

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

FUCHS

:: MORE INFORMATION

Citation

Metge F, Czaja-Hasse LF, Reinhardt R, Dieterich C.
FUCHS-towards full circular RNA characterization using RNAseq.
PeerJ. 2017 Feb 28;5:e2934. doi: 10.7717/peerj.2934. PMID: 28265491; PMCID: PMC5333540.

TSSV 1.1.0 – Characterization of Complex Allelic Variants in pure and mixed Genomes

TSSV 1.1.0

:: DESCRIPTION

TSSV (Targeted characterisation of Short Structural Variation) is a program that does targeted characterisation of short structural variation. It can be used for STR analysis, or any other type of targeted analysis. It characterises any variation between a set of user-defined markers.

::DEVELOPER

TSSV team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

  TSSV

:: MORE INFORMATION

Citation

TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes.
Anvar SY, van der Gaag KJ, van der Heijden JW, Veltrop MH, Vossen RH, de Leeuw RH, Breukel C, Buermans HP, Verbeek JS, de Knijff P, den Dunnen JT, Laros JF.
Bioinformatics. 2014 Jun 15;30(12):1651-9. doi: 10.1093/bioinformatics/btu068

RepeatExplorer2 0.3.8 – Repeat Discovery and Characterization using Graph based Sequence Clustering

RepeatExplorer2 0.3.8

:: DESCRIPTION

RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes.

TAREAN (TAndem REpeat ANalyzer) is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

::DEVELOPER

Laboratory of Molecular Cytogenetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RepeatExplorer2

:: MORE INFORMATION

Citation

Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J.
TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.
Nucleic Acids Res. 2017 Jul 7;45(12):e111. doi: 10.1093/nar/gkx257. PMID: 28402514; PMCID: PMC5499541.

Novák P, Neumann P, Macas J.
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2.
Nat Protoc. 2020 Nov;15(11):3745-3776. doi: 10.1038/s41596-020-0400-y. Epub 2020 Oct 23. PMID: 33097925.

TENET V.1 – Topological Feature-based Target Characterization in Signaling Networks

TENET V.1

:: DESCRIPTION

TENET (Target Characterization using Network Topology) first computes a set of topological features and then leverages a SVM-based approach to identify predictive topological features that characterizes known targets.

::DEVELOPER

Computational Systems Biology Research Group (COSBY)

:: SCREENSHOTS

TENET

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

  TENET

:: MORE INFORMATION

Citation

TENET: Topological Feature-based Target Characterization in Signaling Networks.
Chua HE, Bhowmick SS, Tucker-Kellogg L, Dewey CF Jr.
Bioinformatics. 2015 Jun 16. pii: btv360