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  Bioinformatics links


- Alignment of Sequence Pairs
- Background Info. & News
- Computational Resources
- Databases for other Organisms
- Database Searching by Sequence Similarity
- Gene Expression Databases
- Gene Prediction
- Gene Regulation Resources
- Genome-Scale Analysis
- Genomic Mapping & Mapping Databases
- Human Genome Databases
- Int. Nucleotide Seq. Database Collaboration
- Journals
- Large-scale Genome Analysis 		- Metabolic, Gene Regulatory & Signal Transduction Network Databases
- Misc. Tools & Databases
- Motif & Pattern Finding in Sequences
- Multiple Sequence Alignment
- Other Bioinformatics Resources
- Phylogeny & Taxonomy
- Predictive Methods Using DNA Sequences
- Protein 3D Structure Resources
- Protein Domain Families: Databases & Search Tools
- Protein Sequence Databases
- RNA Analysis
- Structure Databases
- Transmembrane Helix Prediction

Alignment of Sequence Pairs


 button Bayes block aligner
  button BCM Search Launcher: Pairwise sequence alignment
  button SIM: Local similarity program for finding alternative alignment
  button Global alignment programs (GAP, NAP)
  button Likelihood-weighted sequence alignment (lwa)
  button USC Sequence Alignment Server -
  button PipMaker- computes alignments of similar regions in two (long) DNA sequences

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Background Information & News

  button International Society for Computational Biology
  button BiotechFind
  button Futurebiojobs
  button Funding Opportunities
  button DOE Human Genome Project Information
  button National Human Genome Research Institute - NIH
  button Genome Hub @ NHGRI
  button HUGO - The Human Genome Organisation
  button Bioplanet
  button Bioinformatics.org: The Open Lab
  button BioNews Bioinformatics Forum
  button MIT Biology Hypertextbook
  button Online biology textbooks
  button Biochemistry online textbook
  button Cell Biology online tutorials
  button The Bioinformatics Resource
  button BioTech Life Science Dictionary
  button Amino Acid Information - everything you could possibly want to know about amino acids
  button Worthington Enzyme Manual
  button Protein Family Databases
  button PROW - Protein Reviews On the Web
  button RAMBIOS - database of molecular biological review articles
  button GENE QUANTIFICATION web page - info on PCR and other methods for gene expression analysis
  button International Union of Biochemistry and Molecular Biology nomenclature
  button Basal Transcription Factors
  button On-line Medical Dictionary
  button Finding Unusual Words in DNA Sequences
  button NIST Statistics Handbook
  button www.google.com - recommended web search engine

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Computational Resources

  button W3C - World Wide Web Consortium, definitive reference for HTML and other WWW stuff
  button Apache web server documentation
  button PHP information
  button Web Developer's Virtual Library - encyclopedia of web design tutorials, articles and discussions
  button HTML Writers Guild
  button CPAN - PERL modules
  button bioperl - bioinformatics related PERL modules
  button C++ Standard Template Library Programmer's Guide
  button C++ Annotations
  button Dinkum C Library Reference
  button GNU C Library Reference
  button C Tutorial
  button Java Tutorial
  button Numerical Recipes in C and Fortran
  button Matlab Documentation
  button Dictionary of Algorithms, Data Structures, and Problems
  button The Linux Cookbook
  button Alphabetical Directory of Linux Commands
  button TOP500 - list of the world's top 500 supercomputers

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Databases for other Organisms

  button GOLD - Genomes OnLine Database, information on complete and ongoing genome projects
  button The Proteome Databases - yeast, worm, & human, good annotation
  button Mouse Genome Informatics
  button ZFIN - Zebrafish Information Network
  button FlyBase
  button Berkeley Drosophila Genome Project
  button WormBase - C. elegans
  button The Arabidopsis Information Resource
  button DictyBase - Dictyostelium discoideum
  button Saccharomyces Genome Database - yeast
  button PlasmoDB - malaria parasite
  button TIGR Comprehensive Microbial Resource
  button EcoGene - E. coli
  button HIV sequence

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Database Searching by Sequence Similarity

  button BLAST @ NCBI
  button PSI-BLAST @ NCBI
  button FASTA @ EBI
  button Bioccelerator @ EMBL - rigorous Smith-Waterman database search

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Gene Expression Databases

  button HuGE - database of human gene expression using arrays
  button ExpressDB - yeast and E. coli RNA expression data
  button SAGE Genie - gene expression in normal and cancerous human tissues
  button SAGEmap - SAGE tag to gene mapping
  button Bodymap - human and mouse gene expression database using ESTs
  button Stanford Microarray Database

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Gene Prediction
  button Genscan - eukaryotes
  button GeneMark
  button Genie - eukaryotes
  button GLIMMER - prokaryotes
  button tRNAscan - SE 1.1 - search for tRNA genes in genomic sequence
  button GFF (General Feature Format) Specification - a standard format for genomic sequence annotation

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Gene Regulation Resources

  button TRANSFAC - database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors
  button EPD - eukaryotic promoter database
  button DBTSS - DataBase of Transcriptional Start Sites (human)
  button SCPD - Saccharomyces cerevisiae promoter database
  button DCPD - Drosophila Core Promoter Database
  button RegulonDB - a database on transcriptional regulation in E. coli
  button DPInteract - protein binding sites on E. coli DNA
  button PromoterInspector - prediction of promoter regions in mammalian genomic sequences
  button MatInspector - search for transcription factor binding sites
  button Cister - cis-element cluster finder
  button Regulatory Sequence Analysis Tools
  button Kimono - cluster promoter sequences and expression profiles

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Genome-Scale Analysis

  button MBGD - comparative analysis of completely sequenced microbial genomes
  button COGs - phylogenetic classification of orthologous proteins from complete genomes
  button STRING - detect whether a given query gene occurs repeatedly with certain other genes in potential operons
  button Pedant - automatic whole genome annotation
  button GeneCensus - various whole genome comparisons

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Genomic Mapping and Mapping Databases

Data Repositories
  button The Genome DataBase (GDB)
  button National Center for Biotechnology Information
  button Entrez Genomes Division
  button LocusLink
  button GeneMap'99
  button OMIM
  button HomoloGen
  button BLAST
  button ePCR
  button Entrez sequence viewer
  button GenBank
  button Genomic Biology page
  button dbSTS
  button Mouse Genome Informatics (MGD/MGI)

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Resources and Projects
  button Cytogenetic BAC
  button LBNL/UCSF RMC
  button U. of Bari
  button Cytogenetic/YAC data
  button NCI
  button CCAP
  button Infobiogen
  button SERGG
  button Coriell
  button ARKdb

button Animal Genome Database
  button Cedars-Sinai
  button Genetic Linkage CEPH Genotype Database

button CHLC

button Ge´ne´thon

button Marshfield

button MAP-O-MAT

button Rat Genome Database

button Radiation Hybrid RHdb
  button RH Information Page

button Research Genetics

button WICGR RH Maps
  button WICGR GB4 RH Map Server

button SHGC RH Maps
  button SHGC G3 Map Server
  button Sanger Centre GB4/GM Map server
  button WICGR human physical map
  button CEPH/Ge´ne´thon YAC map

button WUGSC home

button TIGR STCs

button UWHTSC STCs
  button WUGSC BAC fingerprints
  button UBGSC mouse BAC fingerprints

button Trask
  button WICGR mouse physical/genetic map
  button DNA Sequence see NCBI links ORNL Genome Channel
  button Integrated and Catalogs UDB

button LDB
  button LDB Sequence-based maps

button eGenome
  button Comparative Mouse Homology Otsuka/Oxford

button rat-mouse-human
  button Human Chromosome 7-mouse map
  button Bovine Genome Database
  button MCW Rat-Mouse-Human

button Mito Emory
  button HUGO Chromosome resources
  button Sanger Centre

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Human Genome Databases
  button Draft Human Genome @ NCBI
  button Draft Human Genome @ UCSC
  button Celera's draft human & Drosophila genomes
  button Ensembl - automatically annotated human genome
  button GDB - Genome Database
  button Mammalian Gene Collection - full-length (open reading frame) sequences for human and mouse
  button STACK - Sequence Tag Alignment and Consensus Knowledgebase
  button GeneCards - human genes, proteins and diseases

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Int. Nucleotide Sequence Database Collaboration
  button

NCBI - National Center for Biotechnology Information (GenBank database and more)
  button

EBI - European Bioinformatics Institute (EMBL database and more)
  button

DDBJ - DNA Data Bank of Japan
  button

Feature Table Definition - the format of entries in these databases
  button

SRS - the Sequence Retrieval System

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Journals
  button Medline / PubMed
  button Web of Science search
  button NEC Research Index
  button Nucleic Acids Research
  button Pacific Symposium on Biocomputing On-line Proceedings

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Large-scale Genome Analysis

NCBI Databases Tools
  button DDD
  button NCBI Gene Expression Omnibus
  button SAGEmap
  button xProfiler

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Software
  button rrayDB
  button Cluster, TreeView, and ScanAlyze
  button CrazyQuant
  button GeneCluster
  button GeneX
  button ScanAlyze; AMAD

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Metabolic, Gene Regulatory & Signal Transduction Network Databases
  button KEGG - Kyoto Encyclopedia of Genes and Genomes
  button BioCarta
  button stke - Signal Transduction Knowledge Environment
  button BIND - Biomolecular Interaction Network Database
  button EcoCyc
  button WIT
  button SPAD - Signaling Pathway Database
  button CSNDB - Cell Signalling Networks Database
  button PathDB
  button Transpath
  button DIP - Database of Interacting Proteins
  button PFBP - Protein Function and Biochemical Networks
  button Alliance for Cellular Signaling

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Miscellaneous Tools & Databases
  button Cancer Genome Anatomy Project
  button HUGO's Human Gene Nomenclature - let's clean up the mess!
  button Gene Ontology Consortium -  a controlled vocabulary of eukaryotic gene roles
  button ACUTS - compilation of Ancient Conserved UnTranslated Sequences
  button UTR database
  button ENZYME - enzyme nomenclature database
  button BRENDA - enzyme database
  button TC-DB - comprehensive classification of membrane transport proteins
  button The SNP Consortium
  button HGBASE - database of sequence variations in the human genome
  button MethDB - DNA methylation database
  button SpliceDB - canonical and non-canonical splice site sequences in mammalian genes
  button SpliceOme - database of intron-exon boundaries
  button InBase - intein database
  button The I.M.A.G.E. Consortium
  button The Dragon Database - batch retrieval and visualization of diverse information about genes
  button The Kabat Database of Sequences of Proteins of Immunological Interest
  button Nelson Lab: Cytochrome C
  button REBASE - restriction enzyme database
  button Chemfinder.com - molecule database
  button Repeatmasker - mask repetitive elements in DNA sequences
  button Tandem Repeats Finder
  button Vienna RNA Package - RNA secondary structure prediction
  button mfold - RNA secondary structure prediction
  button EST parser - find alternative polyadenylation sites in mRNAs, using ESTs
  button UTR-extender - extends missing ends of an mRNA using EST and genome sequence data
  button CpG Islands - predict CpG islands
  button NetStart - prediction of translation start sites in vertebrate and A.thaliana sequences
  button ATGpr - prediction of translation start sites in cDNA sequences
  button SignalP - secretory signal peptide prediction
  button PSORT - prediction of protein sorting signals and transmembrane helices
  button CBS Prediction Servers - prediction of protein subcellular localization and various sites in protein and nucleotide sequences
  button Compute pI/Mw Tool
  button Translate Tool
  button Reverse complement nucleotide sequences
  button Melting - calculate melting temperature for nucleic acid duplexes
  button bend.it - calculate curvature and bendability of a DNA sequence
  button webcutter - detect restriction enzyme cutting sites in DNA sequences
  button Primer3 - pick primers from a DNA sequence
  button Probability Distribution Calculators - normal, chi square, t, F, etc.



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Motif and Pattern Finding in Sequences
  button Gibbs Motif Sampler - identification of conserved motifs in DNA or protein sequences
  button AlignACE Homepage - gene regulatory motif finding
  button MEME  - motif discovery and search in protein and DNA sequences
  button SAM - tools for creating and using Hidden Markov Models
  button Pratt - discover patterns in unaligned protein sequences



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Multiple Sequence Alignment
  button T-COFFEE - multiple sequence alignment
  button ClustalW @ EBI - multiple sequence alignment
  button MSA 2.1 - optimal multiple sequence alignment using the Carrillo-Lipman method
  button BOXSHADE - pretty printing and shading of multiple alignments
  button PRALINE
  button MACAW, a workbench for multiple alignment construction and analysis
  button Spidey - an mRNA-to-genomic alignment program
  button Wise2 - align a protein or profile HMM against genomic sequence to predict a gene structure, and related tools
  button VISTA - align + detect conserved regions in long genomic sequences
  button myGodzilla - align a sequence to its ortholog in the human genome
  button Parallel PRRN progressive global alignment



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Other Bioinformatics Resources
  button NAR database list
  button BioBencHelper
  button SoftwareSeek - lots of downloadable software
  button GenomeWeb
  button Chris Smith's links
  button Amos' links
  button ExPASy Proteomics tools
  button Atelier Bioinformatique
  button Biology WorkBench
  button BCM Search Launcher
  button MolBiol.Net
  button BMERC



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Phylogeny & Taxonomy
  button The Tree of Life
  button Species 2000 - index of the world's known species
  button TreeBASE - a database of phylogenetic knowledge
  button PHYLIP - package of programs for inferring phylogenies
  button TreeView - user friendly tree displaying for Macs & Windows
  button Compilation of available phylogeny programs
  button BLAST2 & Orthologue Search
  button CLUSTAL W
  button GeneDoc
  button GeneTree
  button PhyloBLAST
  button Phylogenetic Resources
  button PUZZLEBOOT
  button ReadSeq
  button RDP Tree
  button WebPHYLIP



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Predictive Methods Using DNA Sequences
  button Banbury Cross
  button FGENEH
  button GeneID
  button GeneMachine
  button GeneParser
  button GENSCAN
  button Genotator
  button G RAIL
  button GRAIL-EXP
  button HMMgene
  button MZEF
  button PROCRUSTES
  button RepeatMasker
  button Sputnik



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Protein 3D Structure Resources
  button PDB - protein 3D structure database
  button RasMol / Protein Explorer - molecule 3D structure viewers
  button SCOP - Structural Classification Of Proteins
  button UCL BSM CATH classification
  button The DALI Domain Database
  button FSSP - fold classification based on structure-structure alignment of proteins
  button SWISS-MODEL - homology modeling server
  button Structure Prediction Meta-server
  button K2 - protein structure alignment
  button DALI - 3D structure alignment server
  button DSSP - defines secondary structure and solvent exposure from 3D coordinates
  button HSSP Database - Homology-derived Secondary Structure of Proteins
  button PredictProtein & PHD - predict secondary structure, solvent accessibility, transmembrane helices, and other stuff
  button Jpred2 - protein secondary structure prediction
  button PSIpred (& MEMSAT & GenTHREADER) - protein secondary structure prediction (& transmembrane helix prediction & tertiary structure prediction by threading)



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Protein Domain Families: Databases and Search Tools
  button InterPro - integration of Pfam, PRINTS, PROSITE, SWISS-PROT + TrEMBL
  button PROSITE - database of protein families and domains
  button Pfam - alignments and hidden Markov models covering many common protein domains
  button SMART - analysis of domains in proteins
  button ProDom - protein domain database
  button PRINTS Database - groups of conserved motifs used to characterise protein families
  button Blocks - multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins
  button Protein Domain Profile Analysis @ BMERC - search a library of profiles with a protein sequence
  button TIGRFAMs - yet more protein families based on Hidden Markov Models



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Protein Sequence Databases
  button SWISS-PROT & TrEMBL - annotated protein sequence database and computer annotated supplement PIR - Protein Information Resource
  button MIPS - Munich Information centre for Protein Sequences
 

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RNA Analysis
  button 5S Ribosomal RNA data bank
  button Comparative RNA Web site
  button GenLang linguistic sequence analyzer
  button Gobase for mitochondrial sequences
  button Intron analysis—Saccharomyces cerevisiae
  button tRNA genes, higher plant mitochondria
  button MFOLD minimum energy RNA configuration
  button Nucleic acid database and structure resource
  button Pseudobase–pseudoknot database maintained by E. van Batenburg, Leiden University
  button Ribonuclease P database Web site
  button Ribosomal RNA database project (RDP II)
  button Ribosomal RNA mutation databases
  button RiboWeb Project–3D models of E. coli 30S ribosomal subunit and 16s rRNA
  button RNA aptamer sequence database (University of Texas)
  button RNA editing Web site, UCLA
  button RNA secondary structures, Group I introns, 16S rRNA, 23S rRNA
  button RNA structure database
  button rRNA–Database of ribosomal subunit sequences
  button Signal recognition particle database
  button tmRNA database
  button tRNAscan-SE search server
  button uRNA database
  button Vienna RNA package for RNA secondary structure prediction and comparison
  button Viroid and viroid-like RNA sequences



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Structure Databases
  button BIND
  button Imagemagick
  button mmCif Project
  button National Center for Biotechnology Information (NCBI)
  button NCBI Toolkit
  button Nucleic Acids Database (NDB)
  button Protein Data Bank at RCSB
  button RasMol
  button SwissPDB Viewer/Deep View
  button WebMol

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Transmembrane Helix Prediction
  button TMHMM
  button SOSUI
  button TMpred

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Supported by Kansas IDeA Network of Biomedical Research Excellence (K-INBRE).  ©2005 Kansas state University Bioinformatics Center. Web site design and construction:Suzhi Wang. All right reserved.