nextNEOpi v1.2 – NeoEpitope predictions Nextflow Pipeline

nextNEOpi v1.2

:: DESCRIPTION

nextNEOpi is a comprehensive pipeline for computational neoantigen prediction.

::DEVELOPER

the Institute of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

nextNEOpi

:: MORE INFORMATION

Citation

Rieder D, Fotakis G, Ausserhofer M, René G, Paster W, Trajanoski Z, Finotello F.
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction.
Bioinformatics. 2021 Nov 12:btab759. doi: 10.1093/bioinformatics/btab759. Epub ahead of print. PMID: 34788790.

PoPS 1.2 – Predictions of Population Structure

PoPS 1.2

:: DESCRIPTION

The POPS program performs inference of ancestry distribution models. It uses a TESS-like interface to compute individual cluster membership and admixture proportions based on multilocus genotype data and their correlation with environmental and geographical variables.

::DEVELOPER

the Computational and Mathematical Biology group in Grenoble

:: SCREENSHOTS

PoPS

:: REQUIREMENTS

  • MacOsX / Windows/ Linux

:: DOWNLOAD

 POPS 

:: MORE INFORMATION

Citation

F. Jay, O. François, M. Blum (2011)
Predictions of Native American Population Structure Using Linguistic Covariates in a Hidden Regression Framework.
PLoS ONE 6(1): e16227

PACCMIT-CDS / PACCMIT – MicroRNA Target Predictions

PACCMIT-CDS / PACCMIT

:: DESCRIPTION

PACCMIT-CDS is a software that finds potential microRNA targets within coding sequences by searching for conserved motifs that are complementary to the microRNA seed region and also overrepresented in comparison with a background model preserving both codon usage and amino acid sequence.

PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets) is a flexible algorithm that filters potential miRNA binding sites in 3’UTR regions by their conservation, accessibility, or both, and then ranks the predictions according to the over-representation with respect to a random background based on a Markov model.

::DEVELOPER

LABORATORY OF THEORETICAL PHYSICAL CHEMISTRY, LCPT

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PACCMIT-CDS

:: MORE INFORMATION

Citation

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences.
Šulc M, Marín RM, Robins HS, Vaníček J.
Nucleic Acids Res. 2015 May 6. pii: gkv457

Searching the coding region for microRNA targets.
Marín RM, Sulc M, Vanícek J.
RNA. 2013 Apr;19(4):467-74. doi: 10.1261/rna.035634.112.

Optimal use of conservation and accessibility filters in microRNA target prediction.
Marín RM, Vanícek J.
PLoS One. 2012;7(2):e32208. doi: 10.1371/journal.pone.0032208.

TransTermHP 2.09 – Transcription Terminator Predictions

TransTermHP 2.09

:: DESCRIPTION

TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TransTermHP

:: MORE INFORMATION

Citation:

C. Kingsford, K. Ayanbule and S.L. Salzberg.
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake.
Genome Biology 8:R22 (2007).