Söding Lab

Login: soedinglab

Company: null

Location: Goettingen, Germany

email:

Blog: https://www.mpibpc.mpg.de/soeding

Members

1. Christian Roth
2. Jessica Andreani
3. Martin Steinegger
4. Milot Mirdita
5. Nikolaos Papadopoulos
6. Saikat Banerjee
7. Salma Sohrabi
8. Stefan Seemayer
9. Susann Vorberg
10. null
11. null

Repositories

BaMMmotif

Bayesian Markov Model motif discovery - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

BaMMmotif2

Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

BaMMserver

Latest updates & bug reporting for the BaMMServer (https://bammmotif.mpibpc.mpg.de)

bamm-suite

De-novo motif discovery and optimization

BaMM_webserver

Webserver for Motif discovery with higher-order Bayesian Markov Models (BaMMs)

bbcontacts

Prediction of beta-strand pairing from direct coupling patterns

b-lore

Bayesian multiple logistic regression for GWAS meta-analysis

CCMpred

Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.

csblast

Context-specific mutation probabilities for protein sequencing searching.

csgraph_mod

Modification of the scipy csgraph class to allow tracking of the visited nodes

ffindex_soedinglab

null

gxpred

Development branch of GxPRED

hhdatabase_cif70

Scripts to generate the pdb70 database for hh-suite on the basis of pdb's mmcif format

hhdatabase_pfam

Scripts to generate the pfam database for hh-suite

hh-suite

Remote protein homology detection suite.

kClust

kClust is a fast and sensitive clustering method for the clustering of protein sequences. It is able to cluster large protein databases down to 20-30% sequence identity. kClust generates a clustering where each cluster is represented by its longest sequence (representative sequence).

merlot

Reconstruct the lineage topology of a scRNA-seq differentiation daatset.

merlot-scripts

Benchmark and plotting scripts for the MERLoT paper

MMseqs

null

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

MMseqs2-App

A GUI for MMseqs2 to run on your workstation or servers

mockinbird

PAR-CLIP data processing pipeline

pdbx

pdbx is a parser module in python for structures of the protein data bank in the mmcif format

PEnG-motif

PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.

prosstt

PRObabilistic Simulations of ScRNA-seq Tree-like Topologies (still under construction)

SNPtarget

A statistical approach to predict enhancer-gene interactions

uniclust-pipeline

null

WIsH

Predict prokaryotic host for phage metagenomic sequences

xxmotif

XXmotif: eXhaustive, weight matriX-based motif discovery in nucleotide sequences