Fundamentals
National Center for Biotechnology Information (NCBI) $^{\color{#3BBB27}\textsf{web}}$ | docs | Centralized repository of biomedical & genetic data
PubMed $^{\color{#3BBB27}\textsf{web}}$ | Literature database focused on biomedicine and health searches abstracts of articles with full text links
PubMed Central (PMC) $^{\color{#3BBB27}\textsf{web}}$ | Component of PubMed contains free full text articles
UniProt $^{\color{#3BBB27}\textsf{web}}$ | Database on proteins and their associated functions
KEGG Database $^{\color{#3BBB27}\textsf{web}}$ | Biological database with entry points into metabolic pathway maps, genes, proteins, biochemical reactions, and more.
BRENDA Enzyme Database $^{\color{#3BBB27}\textsf{web}}$ | Database on enzymes and related information
ExPASy PROSITE $^{\color{#3BBB27}\textsf{web}}$ | Database of protein domains, families, and functional sites.
The European Bioinformatics Institute (EMBL-EBI) $^{\color{#3BBB27}\textsf{web}}$ | Database with bioinformatic information and tools
BioCyc $^{\color{#3BBB27}\textsf{web}}$ | Collection of pathway & genomic databases for model organisms
The Human Protein Atlas $^{\color{#3BBB27}\textsf{web}}$ |
FPbase $^{\color{#3BBB27}\textsf{web}}$ | Fluorescent protein database
Sequence Read Archive (SRA) $^{\color{#3BBB27}\textsf{web}}$ | Largest repository of high through sequencing data
IntAct $^{\color{#3BBB27}\textsf{web}}$ |
GeneCards $^{\color{#3BBB27}\textsf{web}}$ |
Structural
RCSB Protein Data Bank (PDB) $^{\color{#3BBB27}\textsf{web}}$ | Protein database with 3D structural information
RNA
RNAcentral $^{\color{#3BBB27}\textsf{web}}$ | The non-coding RNA sequence database
miRBase $^{\color{#3BBB27}\textsf{web}}$ | Largest updated microRNA database
MirGeneDB $^{\color{#3BBB27}\textsf{web}}$ | Well-annotated microRNA database
miTED $^{\color{#3BBB27}\textsf{web}}$ | MicroRNA Tissue Expression Database
circBase $^{\color{#3BBB27}\textsf{web}}$ | Circular RNA database
circBank $^{\color{#3BBB27}\textsf{web}}$ | Circular RNA database
Genomic tRNA Database $^{\color{#3BBB27}\textsf{web}}$ | Database of automated annotated tRNA gene predictions using tRNAscan-SE
Longevity
Aging Circadian Database $^{\color{#3BBB27}\textsf{web}}$ | Contains circadian gene expression data data from various ages and tissues
Aging Atlas $^{\color{#3BBB27}\textsf{web}}$ | Collection of gene expression data related to the aging process
Taxonomic Specific
Regprecise $^{\color{#3BBB27}\textsf{web}}$ | Contains curated and propagated predictions for regulons in prokaryotic genomes
SGD $^{\color{#3BBB27}\textsf{web}}$ | Comprehensive database on Saccharomyces cerevisiae
TAIR $^{\color{#3BBB27}\textsf{web}}$ | Contains data relevant to Arabidopsis thaliana
EcoCyc $^{\color{#3BBB27}\textsf{web}}$ | Curated database on genome, transcriptional regulation transporters & metabolic pathways in Escherichia coli K-12 MG1655
RegulonDB Database $^{\color{#3BBB27}\textsf{web}}$ | Curated database on transcriptional regulation in Escherichia coli K-12
Miscellaneous
JGI GOLD $^{\color{#3BBB27}\textsf{web}}$ | Collection of metagenomic and genomic data
Atlas of Macromolecules $^{\color{#3BBB27}\textsf{web}}$ | Database containing data on about 160 macromolecules
Bionumbers $^{\color{#3BBB27}\textsf{web}}$ | Describes useful number values in biology
Database Commons $^{\color{#3BBB27}\textsf{web}}$ | Curated catalog of biological databases
General
CoGe $^{\color{#3BBB27}\textsf{web}}$ |
MPI Bioinformatics Toolkit $^{\color{#3BBB27}\textsf{web}}$ |
Softberry $^{\color{#3BBB27}\textsf{web}}$ |
Elixir Bio.tools $^{\color{#3BBB27}\textsf{web}}$ |
Sequence Manipulation Suite (SMS) $^{\color{#3BBB27}\textsf{web}}$ |
SeWeR $^{\color{#3BBB27}\textsf{web}}$ |
Prabi $^{\color{#3BBB27}\textsf{web}}$ |
Galaxy $^{\color{#3BBB27}\textsf{web}}$ |
NEB Tools $^{\color{#3BBB27}\textsf{web}}$ |
RNASeq Pipeline $^{\color{#3BBB27}\textsf{web}}$ |
UGene $^{\color{#FF0000}\textsf{app}}$ |
Jalview $^{\color{#FF0000}\textsf{app}}$ |
Lab Specific
Levin Lab Tools $^{\color{#3BBB27}\textsf{web}}$ |
GrimmLab $^{\color{#3BBB27}\textsf{web}}$ |
Quinlan Lab $^{\color{#3BBB27}\textsf{web}}$ |
Positions various sequences with similar portions in line with one another to observe possible homology
Pairwise Align DNA $^{\color{#3BBB27}\textsf{web}}$ |
Pairwise Align Protein $^{\color{#3BBB27}\textsf{web}}$ |
PIR Pairwise Alignment $^{\color{#3BBB27}\textsf{web}}$ |
LALIGN $^{\color{#3BBB27}\textsf{web}}$ |
Clustal Omega $^{\color{#3BBB27}\textsf{web}}$ |
MultAlin $^{\color{#3BBB27}\textsf{web}}$ |
T-Coffee $^{\color{#3BBB27}\textsf{web}}$ |
EMBL-EBI MSA Tools $^{\color{#3BBB27}\textsf{web}}$ |
MSAReveal $^{\color{#3BBB27}\textsf{web}}$ |
Produces dot plots for comparing sequences
Dotlet JS $^{\color{#3BBB27}\textsf{web}}$ |
Dotmatcher $^{\color{#3BBB27}\textsf{web}}$ |
CoGe: SynMap $^{\color{#3BBB27}\textsf{web}}$ |
CoGe: SynMap3D $^{\color{#3BBB27}\textsf{web}}$ |
Specialized tools for scanning sequences against knowledgebase and specific functional areas of a sequence or genome
BLAST $^{\color{#3BBB27}\textsf{web}}$ | The quintessential tool for identifying sequences
NCBI: ORFfinder $^{\color{#3BBB27}\textsf{web}}$ | Searches for open reading frames in a sequence
tRNAscan-SE $^{\color{#3BBB27}\textsf{web}}$ | Uses predictive software to scan for possible tRNAs
GeneMark gene prediction $^{\color{#3BBB27}\textsf{web}}$ | Implements unsupervised training to identify protein coding genes
FGENESH $^{\color{#3BBB27}\textsf{web}}$ | Gene structure prediction tool
Ribovore $^{\color{#3BBB27}\textsf{web}}$ | A collection of tools for subunit RNA detection
PeCoP $^{\color{#3BBB27}\textsf{web}}$ | A PSI-BLAST tool for finding persistently conserved positions
TargetScanHuman 8.0 $^{\color{#3BBB27}\textsf{web}}$ | Searches for predicted micro RNA targets in mammals
SRAMP $^{\color{#3BBB27}\textsf{web}}$ |
bedtools $^{\color{#D29922}\textsf{cli}}$ |
samtools $^{\color{#D29922}\textsf{cli}}$ |
regtools $^{\color{#D29922}\textsf{cli}}$ |
RSeQC $^{\color{#D29922}\textsf{cli}}$ | An RNA-seq Quality Control Package
WebLogo About $^{\color{#3BBB27}\textsf{web}}$ | Generates sequence logos
Benchling $^{\color{#3BBB27}\textsf{web}}$ | Platform for conducting biotechnology research allowing for easy gene annotation, visualization, and more.
ApE (A Plasmid Editor) $^{\color{#3BBB27}\textsf{web}}$ |
Savvy $^{\color{#3BBB27}\textsf{web}}$ | Website for producing annotated plasmid maps
NUPACK $^{\color{#3BBB27}\textsf{web}}$ | Webserver for analyzing nucleic acid structures
Sequence Massager $^{\color{#3BBB27}\textsf{web}}$ | Allows for easy sequence modification including automatic transcription
Translate $^{\color{#3BBB27}\textsf{web}}$ | Easy tool for converting DNA/RNA sequences into amino acids
ScanProsite $^{\color{#3BBB27}\textsf{web}}$ | Scans sequences against collection of motifs
InterPro $^{\color{#3BBB27}\textsf{web}}$ | Classifies proteins into families using predictive algorithm and has curated databases
NCBI Conserved Domain Search $^{\color{#3BBB27}\textsf{web}}$ | Identifies conserved domains within a sequence
Softberry Tools $^{\color{#3BBB27}\textsf{web}}$ | Suite of tools for scanning for motifs and domains
Multiple Em for Motif Elicitation (MEME) Suite $^{\color{#3BBB27}\textsf{web}}$ | A collection of motif-based analysis tools
Relevant Databases:
SCOP| Structural Classification of Proteins $^{\color{#3BBB27}\textsf{web}}$ | Contains detailed information concerning protein folds and related structures
CATH: Protein Structure Classification Database at UCL $^{\color{#3BBB27}\textsf{web}}$ | Database of protein structures
Conserved Domains Database (CDD) $^{\color{#3BBB27}\textsf{web}}$ | Tools for analyzing conserved domains and protein classifications
COXPRESdb $^{\color{#3BBB27}\textsf{web}}$ | Database with information concerning co-regulated gene relationships
Group of tools for producing 2D & 3D structural data
AlphaFold2 $^{\color{#3BBB27}\textsf{web}}$ |
AlphaFold3 $^{\color{#3BBB27}\textsf{web}}$ |
Swiss-Model $^{\color{#3BBB27}\textsf{web}}$ | 3D protein modeling with similar experimental and predicted models
Protter interactive protein feature visualization $^{\color{#3BBB27}\textsf{web}}$ | 2D protein visualizing tool of polypeptide sequence and predicted cellular location
iCn3D: Web-based 3D Structure Viewer $^{\color{#3BBB27}\textsf{web}}$ | Loads PDB files and generates 3D structures
Cn3D $^{\color{#3BBB27}\textsf{web}}$ | 3D structure viewer
TM-align $^{\color{#3BBB27}\textsf{web}}$ | Algorithm for superpositioning two protein structures using residue-residue alignment
US-align $^{\color{#3BBB27}\textsf{web}}$ | Extended from TM-align and compares 3D structures (proteins, RNA, & DNA)
I-TASSER $^{\color{#3BBB27}\textsf{web}}$ | Agorithm to predict protein structures using a hierarchical approach
RNAstructure $^{\color{#3BBB27}\textsf{web}}$ $^{\color{#FF0000}\textsf{app}}$ $^{\color{#D29922}\textsf{cli}}$ | Contains tools for RNA secondary structure prediction
PDB2PQR $^{\color{#3BBB27}\textsf{web}}$ | Visualize electrostatic potential of a 3D protein
Phyre2 $^{\color{#3BBB27}\textsf{web}}$ | Simple modeling software that allows for one-to-one threading
Rasmol $^{\color{#FF0000}\textsf{app}}$ | Program for molecular model visualization
Swiss-PDB Viewer $^{\color{#3BBB27}\textsf{web}}$ | Viewing software for analyzising several protein structures at once
GRASP $^{\color{#FF0000}\textsf{app}}$ | Macromolecule visualization tool
UCSF Chimera $^{\color{#FF0000}\textsf{app}}$ | Program for visualization of molecular structures
Pymol $^{\color{#FF0000}\textsf{app}}$ | Software for displaying and modifying macromolecules
Jmol $^{\color{#FF0000}\textsf{app}}$ | Viewer for 3D chemical structures
Jpred4 $^{\color{#3BBB27}\textsf{web}}$ | Protein secondary structure predictor
Protein Secondary Structure Tools $^{\color{#3BBB27}\textsf{web}}$ | Group of programs for predicting protein secondary structure
Molecular Graphics Software $^{\color{#3BBB27}\textsf{web}}$ | List of resources for visualizing macromolecules and interactions
MGLtools $^{\color{#FF0000}\textsf{app}}$ | Visualization tool for observing macromolecule structure
ViennaRNA $^{\color{#D29922}\textsf{cli}}$ |
Samson $^{\color{#FF0000}\textsf{app}}$ |
ShapeMapper2 $^{\color{#D29922}\textsf{cli}}$ |
RNAFramework $^{\color{#D29922}\textsf{cli}}$ |
Relevant Databases:
Alphafold $^{\color{#3BBB27}\textsf{web}}$ |
Swiss-Model $^{\color{#3BBB27}\textsf{web}}$ |
RCSB PDB $^{\color{#3BBB27}\textsf{web}}$ |
Primer3Plus $^{\color{#3BBB27}\textsf{web}}$ | Uses Primer3 software to produces primers to detect a given sequence
Primer3 $^{\color{#3BBB27}\textsf{web}}$ | Original software for generating primers for sequences
PrimerX $^{\color{#3BBB27}\textsf{web}}$ | Automates design of mutagenic PCR primers
NEB List of Recognition Specificities $^{\color{#3BBB27}\textsf{web}}$ | Endonuclease recognition sequences and associated enzyme
NEBcutter V2.0 $^{\color{#3BBB27}\textsf{web}}$ | Identify cut sites for a DNA sequence
Seed Viewer $^{\color{#3BBB27}\textsf{web}}$ | Curated genomic data for comparative genomics
IslandViewer 4 $^{\color{#3BBB27}\textsf{web}}$ | Tool for predicting genomic islands
UCSC Genome Browser $^{\color{#3BBB27}\textsf{web}}$ | General genome browser
Ensembl $^{\color{#3BBB27}\textsf{web}}$ | Vertebrate genome browser
Ensembl Bacteria $^{\color{#3BBB27}\textsf{web}}$ | Bacterial genomic data
UCSC Archaeal Genome Browser $^{\color{#3BBB27}\textsf{web}}$ | Archaeal genomic data
Pseudomonas Genome DB $^{\color{#3BBB27}\textsf{web}}$ | Browses pseudomonas genome
MicroScope: MAGE $^{\color{#3BBB27}\textsf{web}}$ | Microbial Genome Annotation & Analysis Platform
Generates phylogenetic trees
-
Phylogeny.fr
$^{\color{#3BBB27}\textsf{web}}$ | Previous version
NGPhylogeny.fr $^{\color{#3BBB27}\textsf{web}}$ |
Simple Phylogeny $^{\color{#3BBB27}\textsf{web}}$ |
SeaView $^{\color{#FF0000}\textsf{app}}$ |
MEGA 11 $^{\color{#FF0000}\textsf{app}}$ |
Simple Phylogeny $^{\color{#3BBB27}\textsf{web}}$ |
SeaView $^{\color{#FF0000}\textsf{app}}$ |
MEGA 11 $^{\color{#FF0000}\textsf{app}}$ |
Phobius $^{\color{#3BBB27}\textsf{web}}$ |
SignalP 5.0 Services DTU Health Tech $^{\color{#3BBB27}\textsf{web}}$ |
TMHMM 2.0 Services DTU Health Tech $^{\color{#3BBB27}\textsf{web}}$ |
TargetP 2.0 Services DTU Health Tech $^{\color{#3BBB27}\textsf{web}}$ |
ExPASy Compute pI/Mw tool $^{\color{#3BBB27}\textsf{web}}$ |
Protein Localization | MBInfo $^{\color{#3BBB27}\textsf{web}}$ |
Immunomedicine Group: Tools >> SIAS $^{\color{#3BBB27}\textsf{web}}$ |
MitoMiner 4.0: Home $^{\color{#3BBB27}\textsf{web}}$ |
PRATT $^{\color{#3BBB27}\textsf{web}}$ |
Tools and packages for conducting metagenomic analysis
MicrobiomeAnalyst $^{\color{#3BBB27}\textsf{web}}$ | Statistical software for analyzing metagenomic data
DADA2 $^{\color{#3BBB27}\textsf{web}}$ | Denoising package for eliminating spurious reads
Mothur $^{\color{#D29922}\textsf{cli}}$ | Denoising package for filtering false reads
Qiime2 $^{\color{#D29922}\textsf{cli}}$ | Suite of tools for metagenomic data processing and analysis
Useful tools for converting different between different filetypes
RNAComposer $^{\color{#3BBB27}\textsf{web}}$ | Converts RNA structure files between different formats
EMBOSS Seqret $^{\color{#3BBB27}\textsf{web}}$ | Tool for reformatting sequence filetypes
Helpful Forums for bioinformatics discussion
Biostars $^{\color{#3BBB27}\textsf{web}}$ | General bioinformatics forum
SEQanswers $^{\color{#3BBB27}\textsf{web}}$ | Sequencing centric forum
Bioinformatics.org $^{\color{#3BBB27}\textsf{web}}$ | General bioinformatics forum
Stack Overflow $^{\color{#3BBB27}\textsf{web}}$ | General programming forum
OmicsForum $^{\color{#3BBB27}\textsf{web}}$ | Community for various analysis tools related to metabolomics, metagenomics, proteomics, and more
QIIME2 Forum $^{\color{#3BBB27}\textsf{web}}$ | Forum for the QIIME2 platform
MicrobesOnline $^{\color{#3BBB27}\textsf{web}}$ | Database centered on microbial data CAUTION Last updated is June 2009
Xfam $^{\color{#3BBB27}\textsf{web}}$ | Decommissioned collection of databases for families of Proteins, DNA, and RNA CAUTION Inactive
RNAmmer 1.2 Server $^{\color{#3BBB27}\textsf{web}}$ | Identified related sequences to ribosomal subunits
GeneBee Motifs $^{\color{#3BBB27}\textsf{web}}$ | Program for identifying motifs within a sequence
Dotlet $^{\color{#3BBB27}\textsf{web}}$ |
General
Python $^{\color{#3BBB27}\textsf{web}}$ |
PyBedtools $^{\color{#3BBB27}\textsf{web}}$ |
Samtools $^{\color{#D29922}\textsf{cli}}$ |
SLURM
UF Research Computing Documentation $^{\color{#3BBB27}\textsf{web}}$ |
Official SLURM Documentation $^{\color{#3BBB27}\textsf{web}}$ |
BenchtopCloning Guides
addgene Cre-lox $^{\color{#3BBB27}\textsf{web}}$ |
Gene Expression Omnibus (GEO) $^{\color{#3BBB27}\textsf{web}}$ |
Harmonizome $^{\color{#3BBB27}\textsf{web}}$ |
Enrichr $^{\color{#3BBB27}\textsf{web}}$ |
https://guides.lib.berkeley.edu/bioinformatics"
https://en.wikipedia.org/wiki/List_of_open-source_bioinformatics_software
https://github.com/pysam-developers/pysam
https://rseqc.sourceforge.net/
https://rnaseq-mats.sourceforge.io/ Multivariate Analysis of Transcript Splicing (MATS) https://github.com/Xinglab/rmats-turbo/tree/v4.2.0
http://www.usadellab.org/cms/?page=trimmomatic
https://cutadapt.readthedocs.io/en/stable/
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - https://mugenomicscore.missouri.edu/PDF/FastQC_Manual.pdf
https://ccb.jhu.edu/software/stringtie/gff.shtml#format - gffread
https://jgi.doe.gov/data-and-tools/software-tools/bbtools/
https://github.com/ncbi/sra-tools
https://github.com/OpenGene/fastp
https://github.com/Hengfu-Yin/IsoSplitter
https://github.com/griffithlab/regtools
https://github.com/TimoLassmann/samstat
https://github.com/sortmerna/sortmerna
https://mafft.cbrc.jp/alignment/software/b
https://daehwankimlab.github.io/hisat2/
https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-aligner http://qualimap.conesalab.org/doc_html/index.html#
https://app.fluorofinder.com/svs_portal
RNA-seq https://github.com/alexdobin/STAR
https://github.com/rajewsky-lab/mirdeep2
https://www.thermofisher.com/order/fluorescence-spectraviewer/#!/ https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorophores.html
https://www.ncbi.nlm.nih.gov/bioproject Bioproject section??!?!?
http://rna.tbi.univie.ac.at//cgi-bin/RNAWebSuite/RNAfold.cgi
http://contra.stanford.edu/contrafold/
ATGpr $^{\color{#3BBB27}\textsf{web}}$ | A program for identifying the initiation codons in cDNA sequences