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Molecular Informatics Resource for the Analysis of Gene Expression - Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics.
 
Multiple Sequence Alignment - Online services for multiple sequence alignment, including ctree, clustalw and msa. Includes sources to build clustalw on your system.
 
NIH BioInformatics and Molecular Analysis Section - Numerous computational tools and resources to unite advances in biology with those in computers, informatics, and networking for the genomic and genetic analysis fields of BioInformatics; division of the Computational Bioscience and Engineering Lab at the Center for Information Technology.
 
Official REBASE Homepage - The restriction enzyme database - from New England Biolabs.
 
PIR-International Protein Sequence Database - produces a comprehensive, non-redundant, and expertly annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research.
 
Protein Structure Prediction Using Web Resources - SPORes is a website for protein structure prediction using the web browser as an interface to software that runs of web servers or other resources available over the world wide web.
 
RNAGENiE - An online program which locates novel RNA genes in genomic DNA.
 
SA National Bioinformatics Institute - SANBI aims to bring genome information, computational biology, and analytical tools to the South African research community. Hosts SA National EMBNet Node, provides links to Sequence Retrieval System (SRS), GeneKraal, and TB Genomes Analysis Server. Research in Sequence Tag Alignment and Consensus Knowledgebase (STACK). Databases include BLAST search in Mycobacterium genome.
 
SUPERFAMILY HMM library for Structural Assignments to protein sequences and Genomes - This server is a Hidden Markov Model library providing 3 services: sequence searching, sequence alignments and genome assignments.
 
Searching GenBank - Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).
 
Sequence Analysis (Bielefeld University Bioinformatics Server) - Collection of sequence analysis tools.
 
Sequence Analysis Software - Several basic online software tools for DNA sequence analysis - from Attotron Biosensor Corp.
 
TRANSFAC-The Transcription Factor Database - Very thorough compilation of transcriptional regulatory protein factors & their cognate gene promoter elements along with DNA sequence search & analysis programs - from GBF, Braunschweig, Germany.
 
The XEMBL Project - XEMBL provides access to the EMBL/GenBank/DDBJ Nucleotide Sequence Database, providing output in various XML standards.
 
Transcription Element Search Software (TESS) - Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn.
 
Transterm - a database of mRNA regions and motifs - Transterm - an interactive database of mRNA regions and motifs from all species and genomes. Users can browse the pre-computed data tables, search the sequence databases or search their own sequences.
 
Verbumculus Genetic Sequence Analyzer - An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Executable for Sparc-Solaris, Sparc-Intel or Linux-Intel. Also available as a Java applet.
 
Virtual Genome Center - Online computational resources for PCR primer selection, similarity searching- from the Univ. of Minnesota.
 
genomesapiens.org - presents the HIGH database, a curated annotation of human DNA regions that are proven to code for Immunoglobulin-superfamily proteins.
 
 
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