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Bioinformatics Online Resources

This page is aimed at highlighting especially useful bioinformatics web-services.  Due to the sheer volume of tools out there, this page cannot ever be comprehensive. Rather, this site is aimed at useful rapid widgets that can save you time and effort.

 

Some other groups work to maintain comprehensive tool databases.

 

“Resource Resources”

Online Bioinformatics Resources Collection

Online Analysis Tools

Both of these sites have huge lists and descriptions of useful widgets

 

Benchmarking Studies and Methods Overviews

(work in progress)

There are often many competing programs for performing the same task.  Benchmarking studies are invaluable resources for selecting which program to use.

Comparison of Accuracy of Current Phylogenetic Tree-Building Programs

Comparison of Denoising Programs for 16S Amplicon Library Analysis

Also demonstrates the superiority of denoising approaches vs. classical alignment-based clustering approaches

Comparing Metagenome Assembly Tools

Spoiler: metaSPAdes, MEGAHIT, and IBDA-UD are all good, but which is superior depends on the community.  Other assemblers are very poor in comparison.

Comparing and Contrasting Functional Annotation Systems

In-depth Comparison of KEGG and MetaCyc Systems

Metagenomic Read Classifiers

Microbiome Data as Compositional Data

Overview of Compositional Analyses for Amplicon Libraries and Transcriptomes

Overview of Microbiome Study Design Concepts

 

 

Multifunctional Sites

EMBL-EBI Tools

A suite of fundamental sequence search and manipulation tools.  Aligning, annotating, translating, etc.  This is my new go to for general low-throughput work / exploratory analysis.

 

Soft Berry

A huge humber of useful tools.  Of note is BPROM, a bacterial promoter search tool.

 

EUPathDB

The Eukaryotic Pathogens Database Resources page is a Galaxy instance which hosts a variety of tools.  Highlights are an OrthoMCL pipeline (Markov protein clustering) and many RNA-seq tools.  There are several other useful widgets in here also.

HIV Database at Los Alamos National Labs

Many general use tools for use here, mostly aimed at alignments and preparation for tree-building.  A fun find was Pixel, which makes a picture from an ailgnment.

Functional Annotation

EggNOG

There are several web-based annotation systems out there to choose from.  EggNOG is mentioned here because it is extremely fast and will provide, in addition to it’s own functional annotations (NOGs), COG, KEGG, and pfam all in one click (via the “sequence mapper” tool).  It’s a great first-line function and orthology exploration tool.

WebMGA

A fast and free service for annotating proteins using a variety of systems (COG, pfam, TIGRFAM, prk).  Users can submit many proteins at a time (I haven’t found the upper limit yet!)

GhostKOALA

A “fast” KEGG orthology annotation system.  The only reliable way I have found to get your own KEGG annotations… EggNOG will do it, but it has limitations.  The turn-around time is often several days, but there is no limit on how many proteins can be submitted. A similar system for smaller protein sets, BlastKOALA, is also available. There is a new HMM-model-based system also, called KofamKOALA.

 

Phylogeny

Interactive Tree of Live (IToL)

The easiest way to generate high-quality, customized phylogenetic tree graphics from tree files (such as *.nwk).  

MAFFT webserver

Alignment of very large and diverse sequence sets is a challenging computational task.  The MAFFT team maintains a powerful and easy to use webserver for using their program.  Also provided are clear help files.

CIPRES

Free supercomputer on the XSEDE system with GUI-based interfaces of all of the best open-source alignment and tree-building tools. New algorithms are added regularly.

BOOSTER-BOOtstrap support by TransfER

This group hosts a server that implements their new algorithm for an updated Feselstein Bootstrapping which is adapted for large (100+) phylogenetic trees.  Just upload your best tree and the file with bootstrap trees and the site will create new “transfer bootstrap” values.  This algorithm was detailed in a recent Nature Methods publication.

MiGA

The Microbial Genomes Atlas (MiGA) is a web-tool (also downloadable and usable locally) which will perform rapid whole genome taxonomy explorations via ANI and AAI calculations.  The web server maintains several very useful databases, such as the RefSeq representatives and TARA Oceans datasets.

W-IQ-TREE

IQ-TREE is a fairly new program for building ML-trees.  There are potentially many innovations over other available programs (i.e. RaxML).  W-IQ-TREE is a free computer cluster and web interface devoted to this program; while easy to use and generally free from traffic, user RAM and time limits are quite narrow. IQ-TREE was also recently installed at CIPRES, where wall times and RAM are very generous.

 

Other

EnviPath

A database of biodegradation pathways, hand-curated, searchable by reaction or compound.

 

Last updated May 3, 2019