BioClass – tool for Biomedical Text Classification

BioClass

:: DESCRIPTION

BioClass is a tool for biomedical text classification. Through it, a researcher can split a document set, directly related with a specific topic, into relevant or irrelevant documents. BioClass also supports several algorithms in order to increase the classification process efficiency and provides a set of powerful interfaces to analyse, filter and compare obtained results. In addition, all the operations than can be performed in BioClass are connected between them, so that the classification process is completely guided.

::DEVELOPER

SING Group.

:: SCREENSHOTS

BioClass

:: REQUIREMENTS

  • Linux / Windows
  • java

:: DOWNLOAD

 BioClass

:: MORE INFORMATION

SRCP 1.0 – Sequence Read Classification Pipeline

SRCP 1.0

:: DESCRIPTION

The SRCP is a high-throughput, automated data analysis pipeline that is used to classify genomic shotgun reads into functional/descriptive sequence categories. It represents a powerful means of rapidly describing the sequence content of a genome and a standardized method for estimating gene/repeat enrichment or reduction afforded by Cot filtration, CBCS, and/or other reduced-representation sequencing (RRS) techniques

:: DEVELOPER

the Institute for Genomics, Biocomputing & Biotechnology (IGBB).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 SRCP

:: MORE INFORMATION

Citation

Anal Biochem. 2008 Feb 1;373(1):78-87.
An automated, high-throughput sequence read classification pipeline for preliminary genome characterization.
Chouvarine P, Saha S, Peterson DG.

DomClust – Hierarchical Clustering for Orthologous Domain Classification

DomClust

:: DESCRIPTION

DomClust is an effective tool for orthologous grouping in multiple genomes, which is a crucial first step in large-scale comparative genomics.

::DEVELOPER

Ikuo Uchiyama (uchiyama@nibb.ac.jp)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • C Compiler

:: DOWNLOAD

 DomClust

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2006 Jan 25;34(2):647-58.
Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes.
Uchiyama I.

Tiara 1.0.2 – a tool for DNA sequence Classification

Tiara 1.0.2

:: DESCRIPTION

Tiara is a deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch.

::DEVELOPER

Institute of Evolutionary Biology, University of Warsaw

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

Tiara

:: MORE INFORMATION

Citation:

Karlicki M, Antonowicz S, Karnkowska A.
Tiara: Deep learning-based classification system for eukaryotic sequences.
Bioinformatics. 2021 Sep 27:btab672. doi: 10.1093/bioinformatics/btab672. Epub ahead of print. PMID: 34570171.

Kinannote 1.0 – Protein Kinase Identification and Classification

Kinannote 1.0

:: DESCRIPTION

Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes.

::DEVELOPER

Kinannote team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • hmmer 2
  • Blast 2.24

:: DOWNLOAD

  Kinannote

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 1;29(19):2387-94. doi: 10.1093/bioinformatics/btt419. Epub 2013 Jul 31.
Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.
Goldberg JM, Griggs AD, Smith JL, Haas BJ, Wortman JR, Zeng Q.

GeneSelector 1.0 – Find Small subset of Genes for Classification of Expression data

GeneSelector 1.0

:: DESCRIPTION

GeneSelector finds a small subset of genes for classification of expression data.

::DEVELOPER

Ari Frank. @Laboratory of Computational Biology , Technion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GeneSelector

:: MORE INFORMATION

StoatyDive v1.1.0 – Evaluation and Classification of Peak Profiles for Sequencing data

StoatyDive v1.1.0

:: DESCRIPTION

StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets. It can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data.

::DEVELOPER

Bioinformatics Group Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

StoatyDive

:: MORE INFORMATION

Citation

Heyl F, Backofen R.
StoatyDive: Evaluation and classification of peak profiles for sequencing data.
Gigascience. 2021 Jun 18;10(6):giab045. doi: 10.1093/gigascience/giab045. PMID: 34143874; PMCID: PMC8212874.

AUDACITY 0.2 – AUtozygosity iDentification And ClassIfication Tool

AUDACITY 0.2

:: DESCRIPTION

AUDACITY is novel computational approach for the identification of Runs of Homozygosity by using VCF files from whole-exome and whole-genome sequencing data generated by second generation sequencing technologies.

::DEVELOPER

AUDACITY team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Linux

:: DOWNLOAD

AUDACITY 

:: MORE INFORMATION

Citation

Magi A, Giangregorio T, Semeraro R, Carangelo G, Palombo F, Romeo G, Seri M, Pippucci T.
AUDACITY: A comprehensive approach for the detection and classification of Runs of Homozygosity in medical and population genomics.
Comput Struct Biotechnol J. 2020 Jul 14;18:1956-1967. doi: 10.1016/j.csbj.2020.07.003. PMID: 32774790; PMCID: PMC7394861.

ChroMoS – SNP Classification, Prioritization and Functional Interpretation

ChroMoS

:: DESCRIPTION

ChroMoS (Chromatin Modified SNPs) combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect.

::DEVELOPER

Bioinformatics and Next Generation Sequencing Group; Max Planck Institute of Immunobiology and Epigenetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation.
Barenboim M, Manke T.
Bioinformatics. 2013 Sep 1;29(17):2197-8. doi: 10.1093/bioinformatics/btt356.

WGSQuikr 1.0.0 – Whole-genome Shotgun Metagenomic Classification

WGSQuikr 1.0.0

:: DESCRIPTION

WGSQuikr is a very rapid, whole-genome shotgun metagenomic reconstruction.

::DEVELOPER

WGSQuikr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows
  • MatLab

:: DOWNLOAD

 WGSQuikr

:: MORE INFORMATION

Citation

PLoS One. 2014 Mar 13;9(3):e91784. doi: 10.1371/journal.pone.0091784. eCollection 2014.
WGSQuikr: fast whole-genome shotgun metagenomic classification.
Koslicki D, Foucart S, Rosen G.