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Bioinformatics links      



  Other K-INBRE links



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K-INBRE main page

button Wichita Bioinformatics

button KUMC Bioinformatics

button KU Lawrence Bioinformatics

button KUMC microarray facility


  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

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