RIPCAL 2.0 – Analysis of RIP in Fungal Genomic DNA Repeats

RIPCAL 2.0

:: DESCRIPTION

RIPCAL is a bioinformatics tool for the analysis of repeat-induced point mutation (RIP) of fungi.

::DEVELOPER

Dr James Hane

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl
:: DOWNLOAD

 RIPCAL

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Nov 24;11:655. doi: 10.1186/1471-2164-11-655.
In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes.
Hane JK1, Oliver RP.

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.
Hane JK, Oliver RP.
BMC Bioinformatics. 2008 Nov 12;9:478. doi: 10.1186/1471-2105-9-478.

CodingQuarry 2.0 – Fungal Gene Prediction

CodingQuarry 2.0

:: DESCRIPTION

CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts.

::DEVELOPER

Alison Testa: 13392554@student.curtin.edu.au

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
:: DOWNLOAD

  CodingQuarry

:: MORE INFORMATION

Citation

BMC Genomics. 2015 Dec;16(1):1344. doi: 10.1186/s12864-015-1344-4. Epub 2015 Mar 11.
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.
Testa AC1, Hane JK, Ellwood SR, Oliver RP.

ChimeraChecker V1.1 – Chimera Checker for Fungal ITS Region

ChimeraChecker V1.1

:: DESCRIPTION

ChimeraChecker is a blast-based open source software package to examine newly generated fungal internal transcribed spacer (ITS) sequences for the presence of potentially chimeric elements in batch mode.

::DEVELOPER

Henrik Nilsson (henrik dot nilsson at dpes dot gu dot se)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ChimeraChecker

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2010 Nov;10(6):1076-81. doi: 10.1111/j.1755-0998.2010.02850.x.
An open source chimera checker for the fungal ITS region.
Nilsson RH1, Abarenkov K, Veldre V, Nylinder S, DE Wit P, Brosché S, Alfredsson JF, Ryberg M, Kristiansson E.

Bagheera – Predicting Fungal CUG Codon Translation in Yeast

Bagheera

:: DESCRIPTION

Bagheera is a web server of prediction of genes in yeast species by providing the correct CUG decoding scheme , that allows determining the most probable CUG codon translation for a given transcriptome or genome assembly based on extensive reference data.

::DEVELOPER

kollmar_group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2014 May 29;15:411. doi: 10.1186/1471-2164-15-411.
Predicting the fungal CUG codon translation with Bagheera.
Mühlhausen S, Kollmar M

MultiLoc2 20091026 – Predict Animal, Plant and Fungal Protein Subcellular Localization

MultiLoc2 20091026

:: DESCRIPTION

MultiLoc2 predicts animal, plant and fungal protein subcellularlocalizations by integrating phylogeny and Gene Ontology terms to the new version of the software.

::DEVELOPER

APPLIED BIOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MultiLoc2

:: MORE INFORMATION

Citation

Blum, T, Briesemeister, S, and Kohlbacher, O (2009).
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
BMC Bioinformatics, 10:274.