Types of links listed on this page:
Integrated -- "Genomes-plus" -- Databases
- The National Center for Biotechnology Information
- This is the top of the NCBI heirarchy -- your gateway to the various search services and databases they offer.
- Genbank growth stats can be found at /genbank/release.notes
- NCBI's FTP Site
- NCBI's Entrez Browser, the user-friendly, massively hyper-linked unification of all their databases
- European Bioinformatics Institute (EBI) Home Page
- Human mitochodrial genome database
- complete with figures, information on sequence, function, markers, mutations and diseases, and more... (contributed by Belinda Sly)
- The Arabidopsis Information Management system
- Arabidopsis stocks, references, researchers, sequences, YACs, and other goodies (contributed by Kan Nobuta)
- MaizeDB
- ...a little garish, but...here's your source for information about Zea mays and its fans, plus links to other plant information servers (contributed by Kan Nobuta)
- Kyoto Encyclopedia of Genes and Genomes
- integration of metabolic and sequence information
- WIT ("What Is There?")
- a similar integration of metabolism and sequence, successor to PUMA
- Overview of the E. coli Metabolic Map
-
Genome Sequences (and other genome data)
- Saccharomyces cerevisiae
- Saccharomyces Genomic Information Resource
- SGD (Saccharomyces Genome Data), searchable by BLAST
- TIGR Microbial Database -- gateway to data on all the sequenced beasties (not only those done by TIGR)
- The Organellar Genome Megasequencing Project
- Genome programs
- Organellar genomes sequenced by OGMP
- mitochondrial genomes in genbank
- chloroplast genomes sequenced
- Rhodobacter genome
- Entrez database of genome maps
- Gobase Home Page
- DOGS - Database Of Genome Sizes
- Terry Gaasterland's MAGPIE genome sequences list (with links to PUMA)
Other Sequence Databases
- Swiss-Prot
- ...and ProtoMap, a database that graphically presents the relationships between the protein families in Swiss-Prot
- Group I Intron Database
- TIGR Database (TDB)
- vector sequence database
- Ribosomal RNA Database Project
- The RDP Home Page
- ...and the VandePeer/ DeRijk/DeWachter rRNA WWW Server
- Kabat Database
- A database of sequences of immunological interest
- hovergen
- a compilation of HOmologous VERtebrate GENes
- The Genome Database (this site is no longer actively maintained, as I understand it...)
- and its home page
- ...intro.html
- GenQuest - The Q server
- OWL-Web
- PIR - The Protein Information Resource
Bibliographic Databases
- ...see the links on my Resources page
- Two sites that do it all! (or pretty close...):
- NCSA's Biology Workbench
- Baylor College of Medicine's Biologists's Control Panel
- Sequence translating, reverse-complementing, and
restriction-site analysis:
- Sequence Utilities at the Baylor College of Medicine (BCM)
- WebGene
- translations, ORF identification, and restriction-site analysis
- (created by Tongjia Yin, recently of the Palmer Lab)
- Format conversion (at tuliptree)
- Integration of gaps and introns in protein and DNA sequences (at tuliptree)
- WebCutter
- only for restriction-site analysis
- REBASE Home Page
- DNASTAR
- DNA Sequence Translation at ALCES
- Oligonucleotide/Primer analysis
- ABIM Online analysis tools
- The Primer Generator
- Oligo Calculator
- Dot plots:
- Large Dot Plots at ALCES
- Format conversion:
- BCM Sequence Utilities
- Multiple alignments:
- Aides to sequence alignment
- ClustalX Help
- plain text on-line help for ClustalW at Wash. U.
- A Gentle Guide to Multiple Alignment
- ALGORITHMS FOR MULTIPLE SEQUENCE ALIGNMENTS
- AllAll: Related peptide sequences
- Brian Golding's Brian's 721 Page
- ...and his guide to alignments
- Karl Kjer's paper on using structure as an alignement guide for rRNA alignments
- GeneDoc's Purpose and Features
- Lachlan H. Bell's intro to GDE
- ...and another treatment of The Genetic Data Environment
- Multalin interface page by Tim Downs
- Scoring Matrices used in alignments
- The C687 introduction to sequence alignment
- ...and an online tutorial on database searching and sequence alignment for the same class
- Baylor's Alignment Utilities
- IBCP WWW server form
- CINEMA (is Java-based, so requires Netscape 3)
- SeaView
- Tuneup Alignment Submission Form
- BOXSHADE server
- BLOCK Formatter
- Phylogenetic analysis: I haven't been able to try these URLs out yet, so I'm not positive about this, but I predict that you will probably want to run your phylogenetic analyses on a personal computer or UNIX box...
- PHYLIP analyses at the National University of
Singapore
- last time I checked, you couldn't change any of the default settings...
- PHYLIP bootstrapping at the Institut Pasteur
- TREEGEN:tree generation from distance data
- Sites with information about (non-on-line) phylogenetic analysis software
- PHYLIP Home Page
- Joe Felsenstein's list of Other Phylogeny Programs
- Joe Felsenstein's guide to Phylogeny Programs:MEGA
- The Maddisons' list of Phylogenetic Analysis Computer Programs
- PAUP Condensed Heuristic Search Guide
- Brian Golding's guide to Reconstructing Phylogenies
- The PUZZLE Software
- Ziheng Yang's PAML
- Protein structure information and prediction
- Amino Acid Properties
- Image Library of Biological Macromolecules
- ec-enzyme list
- Image Library of Biological Macromolecules
- EMBL Dali: email server for 3-D protein structure database searches
- PDB WWW Home Page
- Form for PDB query
- Secondary structure prediction:
- PREDATOR Documentation
- The PredictProtein server
- BCM Search Launcher
- RNA structure prediction
- The L585 introduction to sequence analysis tools
- a short guide to tools (mostly ones I've used) useful for sequence manipulation, alignment, and phylogenetic analysis, with sections for UNIX, for personal computers, and the Web
The page you are viewing, http://sunflower.bio.indiana.edu/~pkuhlman/hot.links.sequence.html, was last modified on April 28, 1998.
This page is the creation and intellectual property of Peter L. Kuhlman.
If you have any comments or questions on this document, please contact pkuhlman@bio.indiana.edu.
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