Biology: Genomes & Bioinformatics

Bioinformatics Tutorials Series (BITS) by MIT. Getting DNA sequences, using annotation tracks, locating intron-exon boundaries, searching with BLAT, the use of BLAST and related sequences, nucleotide BLAST, and algorithm comparisons.

A database of Drosophila genes & genomes.

The Zebrafish Model Organism Database.

Calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. It aligns the two most similar sequences first, then adds sequences to the alignment in order of similarity.

Dedicated to the analysis of protein sequences and structures from sequence databases & experiments: calculate molecular weight, amino acid composition, atomic charge, search for repeated sections of amino acid sequence in proteins, and color-code protein sequences.

The Genome database provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. The database is organized in six major organism groups: Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids and includes complete chromosomes, organelles and plasmids as well as draft genome assemblies.

ISAAA presents an easy to use database of Biotech/GM crop approvals for various biotechnology stakeholders. It features the Biotech/GM crop events and traits that have been approved for commercialization and planting and/or for import for food and feed use with a short description of the crop and the trait. Entries in the database were sourced principally from Biosafety Clearing House of approving countries and from country regulatory websites.

Search for functional domains of well-characterized proteins, and match sequences with similar sequences found in these domains. Contains info about the domains, including function, proteins that are present, literature references, and controlled vocabulary.

This tool produces the alignment of two given sequences using BLAST engine for local alignment. Pairwise alignments can be performed on nucleic acids or proteins, & algorithm parameters can be changed to customize the alignment.

Provides a wealth of info on Stem Cells: stem cells basics, ethics, U.S. Policy, current research, scientific literature, and more.

SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists WorldWide.

A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures. It seeks the mathematically optimal alignment opposed to hierarchical.

Contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project.

UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in UniProtKB/Swiss-Prot, UniProtKB/TrEMBL.

DDBJ is one of the three summit databanks that construct the International Nucleotide Sequence Database with NCBI (United States) and EBI (Europe).

Contains info for and about biocurators, and links to many model organism databases.

Dedicated to the analysis of protein sequences and structures from sequence databases & experiments: calculate molecular weight, amino acid composition, atomic charge, search for repeated sections of amino acid sequence in proteins, and color-code protein sequences.

The NCBI houses GenBank, the international depository of publicly available DNA sequences. Subsets include databases for Nuceotide, Core Nucleotide and Protein. BLAST allows searchers to use sequence data to find significant similarities.

Provides taxonomically & geographically resolved data on marine life & the ocean environment, software tools for data exploration & analysis. Over 13.9 million records of 81,000 species from 246 databases