Guides: Bioinformatics Resources at Penn: Tools and Software

Genome References

The Genome Reference Consortium
GRC is an international collaboration that maintains reference genomes for humans and some model organisms
UCSC Genome Browser
UCSC Genome Browser is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.
Genome Data Viewer
GDV is a genome browser supporting the exploration and analysis of more than 540 eukaryotic RefSeq genome assemblies.
Emsembl
Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
Integrative Genome Viewer
IGV is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

PFAM
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models.
UniProt
The mission of UniProt is to provide the scientific community with a comprehensive, high quality and freely accessible resource of protein sequence and functional information.
IUPred
A web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content.
TOPCONS
TOPCONS is a web server for consensus prediction of membrane protein topology.

SAMtools
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats
BLAST
BLAST is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA sequences.

Galaxy
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience.
NCBI - All Resources
NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.