ConSurf 2016 – Identification of Functional Regions in Proteins

ConSurf 2016

:: DESCRIPTION

The ConSurf server is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Ashkenazy H., Abadi S., Martz E., Chay O., Mayrose I., Pupko T., and Ben-Tal N. 2016
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
Nucl. Acids Res. 2016; DOI: 10.1093/nar/gkw408; PMID: 27166375

Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. 2010
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
Nucl. Acids Res. 2010; DOI: 10.1093/nar/gkq399; PMID: 20478830

AMIGO2 R2019b – Advanced Modelling and Identification using Global Optimization

AMIGO2 R2019b

:: DESCRIPTION

AMIGO is a multi-platform (Windows and Linux) toolbox which covers all the steps of the iterative identification procedure: local and global sensitivity analysis, local and global ranking of parameters, parameter estimation, identifiability analysis and optimal experimental design.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Matlab

:: DOWNLOAD

 AMIGO

:: MORE INFORMATION

Citation:

AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology.
Balsa-Canto E, Henriques D, Gabor A, Banga JR.
Bioinformatics. 2016 Jul 4. pii: btw411.

Bioinformatics (2011)doi: 10.1093/bioinformatics/btr370 First published online: June 17, 2011
AMIGO, a toolbox for Advanced Model Identification in systems biology using Global Optimization
Eva Balsa-Canto and Julio R. Banga

riboPicker 0.4.3 – Identification and Removal of rRNA-like Sequences.

riboPicker 0.4.3

:: DESCRIPTION

riboPicker is a tool to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic datasets. The tool was designed to process longer-read datasets (150+bp read length), but works on 100+bp reads too.

riboPicker Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 riboPicker

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Feb 1;28(3):433-5. Epub 2011 Dec 6.
Identification and removal of ribosomal RNA sequences from metatranscriptomes.
Schmieder R, Lim YW, Edwards R.

Gimlet 1.3.3 – Analysing Genetic Individual Identification data

Gimlet 1.3.3

:: DESCRIPTION

GIMLET (Genotypic Identification with MultiLocus Tags) is a software dedicated for geneticists who work on individual identification using molecular tags in diploid species.

::DEVELOPER

Nathaniel Valière

:: SCREENSHOTS

Gimlet

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Gimlet

:: MORE INFORMATION

Citation

GIMLET: a computer program for analysing genetic individual identification data
NATHANIEL VALIéRE
Molecular Ecology Notes (2002),Volume 2, Issue 3, pages 377–379, 10.1046/j.1471-8278 .2002.00228.x

DiscoverY – Y-contig Identification from Whole Genome Assemblies

DiscoverY

:: DESCRIPTION

DiscoverY is a tool to shortlist Y-specific contigs from an assembly of male whole genome sequencing data, based on exact k-mer matches with a female.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DiscoverY

:: MORE INFORMATION

Citation:

Rangavittal, S., Stopa, N., Tomaszkiewicz, M. et al.
DiscoverY: A Classifier for Identifying Y Chromosome Sequences in Male Assemblies
BMC Genomics (2019) 20: 641.

RepeatModeler 2.0.1 – de-novo Repeat Family Identification and Modeling package

RepeatModeler 2.0.1

:: DESCRIPTION

RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.

::DEVELOPER

RepeatModeler team – Institute for Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RepeatModeler

:: MORE INFORMATION

Citation

PLoS One, 13 (3), e0193588 2018 Mar 14 eCollection 2018
Superior Ab Initio Identification, Annotation and Characterisation of TEs and Segmental Duplications From Genome Assemblies
Lu Zeng , R Daniel Kortschak , Joy M Raison , Terry Bertozzi , David L Adelson

Reads2Type 2.0 – Rapid Microbial Taxonomy Identification

Reads2Type 2.0

:: DESCRIPTION

Reads2Type is a web-based tool for taxonomy identification based on whole bacterial genome sequence data.

::DEVELOPER

Dhany Saputra

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Reads2Type: a web application for rapid microbial taxonomy identification.
Saputra D, Rasmussen S, Larsen MV, Haddad N, Sperotto MM, Aarestrup FM, Lund O, Sicheritz-Pontén T.
BMC Bioinformatics. 2015 Nov 25;16(1):398.

MERCI – Motif EmeRging and with Classes Identification

MERCI

:: DESCRIPTION

The MERCI motif locator program is called from within MERCI to locate the motifs in the positive and negative sequence set. It can also be called directly to locate the found motifs in a third sequence set by typing

::DEVELOPER

the DTAI research group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ Windows
  • Perl

:: DOWNLOAD

  MERCI

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 1;27(9):1231-8. doi: 10.1093/bioinformatics/btr110. Epub 2011 Mar 3.
Identifying discriminative classification-based motifs in biological sequences.
Vens C1, Rosso MN, Danchin EG.

Alien_hunter 1.7 – Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA

Alien_hunter 1.7

:: DESCRIPTION

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs).

::DEVELOPER

Alien_hunter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Alien_hunter

:: MORE INFORMATION

Citation

Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
Vernikos GS and Parkhill J
Bioinformatics (Oxford, England)2006;22;18;2196-203

miRA 1.2.0 – micro RNA Identification tool

miRA 1.2.0

:: DESCRIPTION

miRA is a new tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations.

::DEVELOPER

Michael Huttner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 miRA

:: MORE INFORMATION

Citation

miRA: adaptable novel miRNA identification in plants using small RNA sequencing data.
Evers M, Huttner M, Dueck A, Meister G, Engelmann JC.
BMC Bioinformatics. 2015 Nov 5;16:370. doi: 10.1186/s12859-015-0798-3.