Bioinformatics and Functional Genomics

Table 16-7. Web servers that provide access to software for identifying repetitive elements in genomic DNA.

Program	Description
RepeatFinder	RepeatFinder a computational system for analysis of repetitive structure of genomic sequences
RepeatMasker	University of Washington Genome Center
RepeatMasker	Server at EMBL
RepeatMasker	Server in Barcelona
RepeatMasker	For zebrafish; at the Wellcome Trust Sanger Instiutte
Censor Server	Genetic Information Research Institute

 

Table 16-8. Web-based databases of noncoding RNA.

Database	Description
Large ribosomal subunit db	structure of lsu ribosomal subunit RNA
Noncoding RNAs database	Various RNA categories
Rfam	RNA family database at the Sanger Institute
Rfam	RNA family database at Washington University
Ribosomal Database Project (RDP)	Provides ribosome related data analysis, rRNAderived phylogenetic trees, and aligned and annotated rRNA sequences.
RNABase	RNA structures
RNA Editing Web Site	On all the various types of RNA editing
Small ribosomal subunit db	A database on the structure of ssu ribosomal subunit RNA
Small RNA database	Small RNAs are broadly defined as the RNAs not directly involved in protein synthesis.
tRNA sequences	Compilation of 550 sequences of tRNAs and 3704 sequences tRNA genes (through 1998).

 

Table 16-9. Algorithms for finding genes in eukaryotic DNA. Abbreviation: HMM, hidden Markov model. A summary of sites is given in http://linkage.rockefeller.edu/wli/gene/.

Program	Description
AAT	Analysis and Automation Tool. Web based server
FgeneH	Predicts exons using linear discriminant functions
FgeneSH	ab initio gene finder
Gene Finder	For human, mouse, Arabidopsis, and fission yeast
GeneParser 2	Identification of protein coding regions in genomic DNA
Genie	Based on HMMs
GenLang	syntactic pattern recognition system; uses computational linguistics to find genes
Genscan	Based on HMMs; rule-based rather than homology based
GenTerpret	From RabbitHutch Biotechnology Corporation
GlimmerM	From TIGR
GlimmerM web server	For Arabidopsis thaliana, Oryza sativa (rice), Plasmodium falciparum (malaria)
GRAIL	One of the most widely used algorithms
MORGAN	A decision tree system for finding genes in vertebrate DNA
PROCRUSTES	Gene Recognition via Spliced Alignment
VEIL	HMM for finding genes in vertebrate DNA
Xpound	A probabilistic model for detecting coding regions

 

Table 16-10. Software for identifying features of promoter regions in genomic DNA.

Program	Description
Ancient conserved untranslated DNA sequences (ACUTS)	analyzes genes from metazoan species (essentially vertebrates, insects and nematods)
AliBaba2	predicts binding sites of transcription factor binding sites in an unknown DNA sequence
Eukaryotic Promoter Database (EPD)	Annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally
FastM	develops models of transcriptional regulatory DNA units (e.g. promoters)
Gene Regulation	Requires log-in
PlantProm	Plant promoter database
rSNP_Guide	Transcription factor binding site database
TRANSFAC	Database of transcription factors, their genomic binding sites and DNA-binding profiles

 

Table 16-11. Web-based databases of chromosomes.

Resource	Comment
Ensembl genome browser	Ideograms for human (Chapter 17), mouse, rat, zebrafish, fugu, and mosquito
The Unified Database for Human Genome Mapping	From the Weizmann Instutite
Human Chromosome-specific databases	From the UK HGMP Resource Centre
Ideogram Album	Human, mouse, and horse ideograms from the University of Washington
Human Chromosome Launchpad	From the Oak Ridge National Laboratory

 

Table 16-12. Web resources for Trypanosome genomics.

Resource	Comment
The Trypanosoma brucei Genome Network	Sponsored by the Wellcome Trust
T.brucei omni Blast Server	Sanger Institute
Trypanosoma cruzi	Genome Initiative Information Server Trypanosoma cruzi Genome Initiative Information Server

 

Table 16-13. Web resources for Leishmania genomics.

Resource	Comment
The Leishmania major Friedlin Genome Project	At the Wellcome Trust Sanger Institute
SBRI	Seattle Biomedical Research Institute
The European Leishmania major Friedlin Genome Sequencing Consortium	A listing of participating laboratories

 

Table 16-14. Genomics resources for Plasmodium falciparum and malaria.

Resource	Comment
PlasmoDB	Main web resource for P. falciparum
Links page	At NCBI
P. falciparum Genome Project	At the Sanger Institute

 

Table 16-17. Genomics resources for Arabidopsis thaliana.

Resource	Comment
TAIR	The Arabidopsis Information Resource
Arabidopsis thaliana Database	At TIGR
Arabidopsis thaliana Project	At MIPS
Arabidopsis genome analysis	At Cold Spring Harbor
SeedGenes	Essential genes

Table 16-18. A variety of databases employ the model from the Generic Model Organism Project (GMOD)(http://www.gmod.org/).

Database	Comment
EcoCyc	Encyclopedia of Escherichia coli Genes and Metabolism
FlyBase	Drosophila site
Mouse Genome Informatics	Main mouse resource
Rat Genome Database (RGD)	Rat resource
SGD	See Chapter 15
TAIR	The Arabidopsis Information Resource
Wormbase

 

Table 16-19. The Genomics Unified Schema (GUS) platform (http://www.gusdb.org/) is used for some organism databases.

Database	Comment
AllGenes	Human and mouse gene index
EPConDB	Endocrine Pancreas Consortium
GeneDB	curated database for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei
PlasmoDB	genomic database for Plasmodium falciparum
RAD	RNA abundance database

 

Table 16-20. Genomics resources for Dictyostelium discoideum.

Resource	Comment
Dictybase	a centralized source for information about Dictyostelium and related organisms
The Dictyostelium Genome Sequencing Project	Baylor College of Medicine
	Institute of Biochemistry I, Cologne
	Dept. Genome Analysis, IMB Jena
	Sanger Institute
Dictyostelium links	NCBI

 

Table 16-26. Genomics resources for the mouse, Mus musculus.

Resource	Comment
Mouse genome project	Baylor College of Medicine
Mouse cytogenetic maps	Mammalian Genetics Unit, Harwell UK
TBASE	The Transgenic/Targeted Mutation Database
Database of Gene Knockouts	At Bioscience.org
Mouse Genetics	An online book by Lee Silver
Mouse mapping	Genome Sciences Centre (Vancouver)
Trans-NIH Mouse Initiative	Comprehensive NIH mouse genomics site
TIGR Mouse Gene Index	At TIGR

 

Table 16-27. Genomics resources for the rat, Rattus norvegicus.

Resource	Comment
Rat Genome Database	Key rat genomics site
Ratmap	Rat Genome Database
NIH Rat Genomics and Genetics	Main NIH rat site
Rat Genome Resources	Central NCBI rat site
TIGR Rat Gene Index	At TIGR

 

Table 16-28. Genomics resources for non-human primates.

Resource	Comment
Chimpanzee Genome Project	Pan troglodytes at Baylor College of Medicine
Project Silver	National Institute of Genetics (Japan)
Primate Cytogenetics Network	Diploid numbers, karyotypes, ideograms