Genome Analysis

ORF: Open reading frame finding

SIM4: Genomic DNA and cDNA alignment to find exon sequene

UCSC Genome Browser: Genome browser for different organisms, including human, mouse, rat, chick, fly, zebrafish and more

VISTA Genome Browser: Whole-genome alignments

LocusLink Report: Catalogue of known genes

Ensembl: Genome browser, annotation of novel genes based on similarity to known gene, and EST

Genescan, TWINSCAN: Gene predication programs

EPD: Promoter prediction, Eukaryotic Promoter Database at EMBL, Heidelberg

Promoter Prediction: Neural Network Promoter Prediction

Sequence Comparison

NCBI BLAST: Sequence comparison

BLAST 2 Sequence: Alignment of two given sequences

BAC Resources

CHORI: BAC Clone ordering, information of RP-BAC vector information

Tools for Molecular Biology

NEBcutter: Restriction digestion analysis

Primo Pro: PCR primer design, including standard PCR, degenerate primer, multiplex PCR, etc.

Mouse Resources

The Jackson Lab: Collection of information for mouse genetics

TBASE: Transgenic/targeted mutation database

Mouse Genome Resources: NCBI mouse genome resources

Gene expression: Gene expression during development in the mouse. This is part of Mouse Genome Informatics.

Embryo Images: Scanning EM images of mouse/human embryos. This is an excellent site to learn mouse development.

EMAP: Mouse 3D atlas

Mouse Brain Library: Mouse brain (adult and E12.5) atlas

High Resolution Atlas