SEED 4.0.0 – Solvation Energy for Exhaustive Docking

SEED 4.0.0

:: DESCRIPTION

SEED is a program for docking libraries of fragments with solvation energy evaluation.The docking approach implemented in the program SEED determines optimal positions and orientations of small-to-medium-sized molecular fragments in the binding site of a rigid protein (hereafter also referred to as receptor) and ranks them according to their binding energy.

::DEVELOPER

Prof. Amedeo Caflisch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SEED

:: MORE INFORMATION

Citation

Majeux N, Scarsi M, Caflisch A
Efficient electrostatic solvation model for protein-fragment docking.
Proteins: Struct. Funct. Genet 42, 256-268, 2001

SEED 1.5.1 – Clustering Next Generation Sequences

SEED 1.5.1

:: DESCRIPTION

SEED is a software for clustering large sets of Next Generation Sequences (NGS) with hundreds of millions of reads in a time and memory efficient manner. Its algorithm joins highly similar sequences into clusters that can differ by up to three mismatches and three overhanging residues.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux/ MacOsX/Windows

:: DOWNLOAD

SEED

:: MORE INFORMATION

Citation

SEED: efficient clustering of next-generation sequences.
Bao E, Jiang T, Kaloshian I, Girke T.
Bioinformatics. 2011 Sep 15;27(18):2502-9. doi: 10.1093/bioinformatics/btr447. Epub 2011 Aug 2.

Seed – Exploring and Visualizing Microbial Community Data

Seed

:: DESCRIPTION

Seed (Simple Exploration of Ecological Datasets) is an R/Shiny package for visualizing ecological data. It provides a visual interface for generating a wide variety of plots, including histograms, scatterplots, bar plots, stacked bar plots, PCoA plots, cluster dendrograms, and heatmaps.

::DEVELOPER

Daniel Beck , Christopher Dennis at christozoan@gmail.com.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

Seed

:: MORE INFORMATION

Citation

Seed: a user-friendly tool for exploring and visualizing microbial community data.
Beck D, Dennis C, Foster JA.
Bioinformatics. 2014 Oct 20. pii: btu693.

Bicluster – Seed-based Biclustering of Gene Expression Data

Bicluster

:: DESCRIPTION

Bicluster is a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner.

::DEVELOPER

AUSTRALIAN PROSTATE CANCER RESEARCH CENTRE.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
java

:: DOWNLOAD

Bicluster

:: MORE INFORMATION

Citation

An J, Liew AW-C, Nelson CC (2012)
Seed-Based Biclustering of Gene Expression Data.
PLoS ONE 7(8): e42431. doi:10.1371/journal.pone.0042431

FSH – Fast Spaced Seed Hashing

FSH

:: DESCRIPTION

FSH exploits the similarity of adjacent spaced seed hash values in an input sequence in order to efficiently compute the next hash.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

FSH

:: MORE INFORMATION

Citation

J Comput Biol 2019 Dec 4
Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing
Enrico Petrucci , Laurent Noé , Cinzia Pizzi , Matteo Comin