internet_links

Home Page	Avian Centers	Biomolecular	Entrez	Evolution
Funding	Gene Analysis	Genomics	Journals	Multifunction
Non-Biology	Nucleic Acid	Ontology	Protein Analysis	References
Search Engines	Suppliers	Microbial


	Frequent ChickDB entry to ChickDb at University of Delaware GoFigure predection of Gene Ontology terms based upon homology HerpesvirusDB access to herpesvirus database at the University of Delaware CoPrDOM predection of co-present domains using Gene Ontology and Interpro Ribosomal Query Page access to environmental ribosomal database at University of Delaware Blast basic, psi and phi blast ExPASy analysis of protein sequences and structures Open Reading Frame find all six open reading frames Psort predicts protein subcellular localization sites from their amino acid sequences

		Entrez a retrieval system for searching several linked databases Nucleotide retrieve nucleotide sequences Protein retrieve protein sequences 3D Structure retrieve solved 3D structures Genomes retrieve compete genome sequences Taxonomy retrieve taxonomic relationships Literature - Pubmed Medminer- an excellent search engine using NLP

Evolution and Phylogeny
Computer Programs 93 phylogeny packages; 16 free servers: list maintained at Washington University
BoxShade nice output of multiple sequence alignmnets
Phylogenetic tree printer a variety of outputs for phylogenetic trees
TreeBase relational database of phylogenetic information; stores phylogenetic trees and the data matrices
Tree of Life multi-authored, distributed Internet project containing information about phylogeny and biodiversity


	Genomics Online Mendelian Inheritance in Man catalog of human genes and genetic disorders.

Gene Analysis
Blast2 (local alginment)
Grail @ Oakridge National Laboratory exon/intron prediction
Global Alignment Align two DNA or protein sequences using Lipman and Pearson's Align program
MatInspector - search for potential binding sites in DNA .
Open Reading Frame -has Blast link
PIBL (local alignment of two nucleic acid sequences)
Repeat Masker -screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query
rRNA Database


	Multifunction Analysis Programs Baylor College of Medicine Search Launcher Biology Workbench - includes CLUSTALW Biotools Comparative Sequence Analysis (SMART) Department of Energy Joint Genome Institute ExPASy France GenomeWeb Molecular Biology Resource National Center for Biotechnology Pasteur SeqWeb - GCG - login required


	Microarray MIT center NHGRI Microarray Project Stanford-Brown Lab Support Vector Machines Eisen Lab


		Nucleic Acid Analysis Restriction Endonuclease Webcutter Restriction Endonuclease Stanford Virtual Genome Center Primer Design MIT Primer 3

Ontology/Signal Transduction Paths Gene Ontology Penn Ontology Human Developmental Anatomy Java Ontology Browser Pathways- excellent, from the Cancer Genome Anatomy Project Signal Transduction Nework Data Base Transpath

	Protein Analysis Amino Acid Structures BlockMaker finds conserved blocks in a group of two or more unaligned protein sequences Cell Signalling Networks data- and knowledge- base for signaling pathways of human cells Dali Protein Domain Dictionary a structural classification of protein domains. Database of Interacting Proteins Myriad Database of Interacting Proteins EcoCyc Encyclopedia of E. coli Genes and Metabolism Enzymes Enzyme nomenclature database Genome Net Server network of database and computational services for genome research Interpro an excellent well integrated DB for motifs etc. KEGG molecular interactions, metabolic pathways, regulatory pathways, and molecular assemblies Motif Searching Search motif libraries for motifs in a query sequence MEME -identify novel motifs by multiple sequence alignment Owl - composite protein sequence database ProDom - analysis of protein domains ProfileScan Motif Scan in a Protein Sequence Propsearch - search by amino acid composition Protein Information Resource - annotated, non-redundant, cross-referenced, protein database Psort - Prediction of protein sorting signals Sanger Pfam Pfam has pre-calculated the domain structure of the proteins in SWISS-PROT SMART - domain search Statistical Analysis of Protein Sequences Structural Classification of Proteins

	Protein Structural Prediction 3DPSSM Hierarchical Protein Structure Superposition Predict Protein-threading Sawted - tertiary structure alignment DOE-UCLA Interactive Threader 2nd Structure NNPREDICT ss-structure Sanger Structure Prediction Coiled Coil Prediction Visualization: Protein Explorer

		Search Engines & Reference Work Alta Vista Entrez Funded Research Medline MIT Hypertextbook - review of biology basics National Center for Biotechnology On Line Dictionary Pedro's BioMolecular Research Tools Protein Database [PDB] SAGE

			Biomolecular Links: Cell & Molecular Biology Online Computational Biology Cold Spring Harbor- animations Genome Biology Harvard Biolabs Microarray Penn Bioinformatics All the Virology on the World Wide Web Washington University Sequencing Center Weizmann Institute

				Basic References and News for Biology/Biochemistry/Molecular Biology Genomics - Global Resource Kimball's Biology Pages Primer on Molecular Genetics The Scientist


	[internet_links] [Journals] [Non Biology] [Funding Resources] [Avian Centers] [Microbial Engineering]