GOtcha 200812 – Prediction of Gene Function by Application of Gene Ontology

GOtcha 200812

:: DESCRIPTION

GOtcha uses sequence similarity searches to associate GO terms with your sequence. These are ranked by probability and displayed graphically on a subtree of Gene Ontology.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GOtcha

:: MORE INFORMATION

Citation

Martin,DMA, Berriman, M and Barton, GJ (2004),
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes,
BMC Bioinformatics, 5:178 (18 November 2004)

gCUP 1.0 – Rapid GPU-based HIV-1 Coreceptor Usage Prediction for Next-Generation Sequencing

gCUP 1.0

:: DESCRIPTION

gCUP: Rapid GPU-based HIV-1 Coreceptor Usage Prediction for Next-Generation Sequencing

::DEVELOPER

Heider Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R
  • NVIDIA

:: DOWNLOAD

 gCUP

:: MORE INFORMATION

Citation

gCUP: Rapid GPU-based HIV-1 Co-Receptor Usage Prediction for Next-Generation Sequencing.
Olejnik M, Steuwer M, Gorlatch S, Heider D.
Bioinformatics. 2014 Aug 13. pii: btu535.

MIKADO 2.0rc4 – Determine and Select the best RNA-Seq Prediction

MIKADO 2.0rc4

:: DESCRIPTION

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

MIKADO

:: MORE INFORMATION

Citation

Gigascience. 2018 Aug 1;7(8). doi: 10.1093/gigascience/giy093.
Leveraging multiple transcriptome assembly methods for improved gene structure annotation.
Venturini L, Caim S, Kaithakottil GG, Mapleson DL, Swarbreck D.

miRNAgFree – microRNA prediction using sRNAseq/miRNAseq/sncRNAseq

miRNAgFree

:: DESCRIPTION

miRNAgFree is a novel microRNA prediction approach based on biogenesis features, such as the known 5’ homogeneity, and duplex mean free energies which does not require a genome assembly.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • VirtualBox.

:: DOWNLOAD

miRNAgFree

:: MORE INFORMATION

 

Isofinder 20140824 – Isochore Computational Prediction

Isofinder 20140824

:: DESCRIPTION

IsoFinder is a software which able to predict isochores at the sequence level.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 Isofinder

:: MORE INFORMATION

Citation:

Oliver JL, Carpena P, Hackenberg M, Bernaola-Galván P.
IsoFinder: computational prediction of isochores in genome sequences.
Nucl. Acids Res. 32, Web Server issue: W287-W292

MiRPlex 0.1 – microRNA Prediction from High-throughput Sequencing data

MiRPlex 0.1

:: DESCRIPTION

MiRPlex is a tool for microRNA prediction from high-throughput sequencing data that requires only small RNA datasets as input.

::DEVELOPER

the RNA Computational Biology group at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

 MiRPlex

:: MORE INFORMATION

Citation

Mapleson, D.; Moxon, S.; Dalmay, T.; Moulton, V.,
MirPlex: A tool for identifying miRNAs in high-throughput sRNA datasets without a genome.
J Exp Zool B Mol Dev Evol. 2013 Jan;320(1):47-56. doi: 10.1002/jez.b.22483. Epub 2012 Nov 26.

HDMP – Human Disease-related miRNA Prediction

HDMP

:: DESCRIPTION

HDMP can predict the disease-related miRNA candidates for 18 human diseases.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2013 Aug 8;8(8):e70204. doi: 10.1371/journal.pone.0070204. eCollection 2013.
Prediction of microRNAs associated with human diseases based on weighted k most similar neighbors.
Xuan P, Han K, Guo M, Guo Y, Li J, Ding J, Liu Y, Dai Q, Li J, Teng Z, Huang Y.

SPRINT 3.0 – Side-chain PRediction INference Toolbox for Multistate Protein Design

SPRINT 3.0

:: DESCRIPTION

SPRINT is a software package that performs computational multistate protein design using state-of-the-art inference on probabilistic graphical models.

::DEVELOPER

Menachem Fromer and Chen Yanover

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SPRINT

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Oct 1;26(19):2466-7. doi: 10.1093/bioinformatics/btq445. Epub 2010 Aug 4.
SPRINT: side-chain prediction inference toolbox for multistate protein design.
Fromer M1, Yanover C, Harel A, Shachar O, Weiss Y, Linial M.

ACEScan 1.0 – Prediction of Conserved Alternatively Spliced Exons from pairs of Conserved Mouse/Human Exons

ACEScan 1.0

:: DESCRIPTION

ACEScan is a webtool of identification and analysis of alternative splicing events conserved in human and mouse.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yeo, G., Van Nostrand, E., Holste, D., Poggio, T. and Burge, C. B. (2005).
Identification and analysis of alternative splicing events conserved in human and mouse.
Proc. Natl. Acad. Sci. USA 102, 2850-2855

GenomeScan 1.0 – Prediction of Gene Structures in Genomic Sequences

GenomeScan 1.0

:: DESCRIPTION

GenomeScan is a program for identifying the exon-intron structures of genes in genomic DNA sequences from a variety of organisms, with a focus on human and other vertebrates.  The algorithm combines two principal sources of information: 1) models of exon-intron and splice signal composition; and 2) sequence similarity information such as BLASTX hits.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yeh, R.-F., Lim, L. P., and Burge, C. B. (2001)
Computational inference of homologous gene structures in the human genome.
Genome Res. 11: 803-816.